def read_geometry(input_file="wannier.win"):
"""Reads the geometry of the wannier calculation"""
ll = read_between("begin unit_cell_cart","end unit_cell_cart",input_file)
a1 = ll[1].split()
a2 = ll[2].split()
a3 = ll[3].split()
# read the unit vectors
a1 = np.array([float(a1[0]),float(a1[1]),float(a1[2])]) # first vector
a2 = np.array([float(a2[0]),float(a2[1]),float(a2[2])]) # second vector
a3 = np.array([float(a3[0]),float(a3[1]),float(a3[2])]) # second vector
g = geometry.geometry()
g.dimensionality = 2
g.has_spin = False
g.has_sublattice = False
g.a1 = a1 # store vector
g.a2 = a2 # store vector
g.a3 = a3 # store vector
# read the coordinates
ll = read_between("begin projections","end projections",input_file)
rs = [] # empty list for positions
g.atoms_have_names = True # Atoms have names
g.atoms_names = [] # initalize
for l in ll:
name = l.split(":")[0] # get name of the atom
r = get_positions(name,input_file) # get positins of the atoms
g.atoms_names += [name]*len(r) # append this names
for i in range(len(r)): # to real coordinates
r[i] = r[i][0]*a1 + r[i][1]*a2 + r[i][2]*a3
rs += r # store positions
g.r = np.array(rs) # store in the class
g.r2xyz() # store also in xyz atributes
g.get_fractional() # fractional coordinates
return g
def read_geometry(input_file="wannier.win"):
"""Reads the geometry of the wannier calculation"""
ll = read_between("begin unit_cell_cart", "end unit_cell_cart", input_file)
a1 = ll[1].split()
a2 = ll[2].split()
a3 = ll[3].split()
# read the unit vectors
a1 = np.array([float(a1[0]), float(a1[1]), float(a1[2])]) # first vector
a2 = np.array([float(a2[0]), float(a2[1]), float(a2[2])]) # second vector
a3 = np.array([float(a3[0]), float(a3[1]), float(a3[2])]) # second vector
g = geometry.geometry()
g.dimensionality = 2
g.has_spin = False
g.has_sublattice = False
g.a1 = a1 # store vector
g.a2 = a2 # store vector
g.a3 = a3 # store vector
# read the coordinates
ll = read_between("begin projections", "end projections", input_file)
rs = [] # empty list for positions
g.atoms_have_names = True # Atoms have names
g.atoms_names = [] # initalize
for l in ll:
name = l.split(":")[0] # get name of the atom
r = get_positions(name, input_file) # get positins of the atoms
g.atoms_names += [name] * len(r) # append this names
for i in range(len(r)): # to real coordinates
r[i] = r[i][0] * a1 + r[i][1] * a2 + r[i][2] * a3
rs += r # store positions
g.r = np.array(rs) # store in the class
g.r2xyz() # store also in xyz atributes
g.get_fractional() # fractional coordinates
return g
def get_transformation_matrix(
d_mmCIF_apo, l_coords_alpha_apo,
d_mmCIF_holo, l_coords_alpha_holo,
):
## structural alignment
## solution that works in all cases
## also for 2d59 and 2d5a, which have residues missing at the Nterm and Cterm, respectively
## first non-?
index1_seq_apo = next((i for i,v in enumerate(d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id']) if v != '?'))
index1_seq_holo = next((i for i,v in enumerate(d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id']) if v != '?'))
## last non-?
index2_seq_apo = len(d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id'])-next((i for i,v in enumerate(reversed(d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id'])) if v != '?'))
index2_seq_holo = len(d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id'])-next((i for i,v in enumerate(reversed(d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id'])) if v != '?'))
## first common non-?
index1_coord_apo = max(0,index1_seq_holo-index1_seq_apo)
index1_coord_holo = max(0,index1_seq_apo-index1_seq_holo)
## last common non-?
index2_coord_apo = len(l_coords_alpha_apo)+min(0,index2_seq_holo-index2_seq_apo)
index2_coord_holo = len(l_coords_alpha_holo)+min(0,index2_seq_apo-index2_seq_holo)
l_coords_alpha_apo = l_coords_alpha_apo[index1_coord_apo:index2_coord_apo]
l_coords_alpha_holo = l_coords_alpha_holo[index1_coord_holo:index2_coord_holo]
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(l_coords_alpha_apo,l_coords_alpha_holo,)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
return tv1, rm, tv2, l_coords_alpha_apo, l_coords_alpha_holo
def createBilinear(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
if len(list_P) != 4:
print("You have to specify 4 markers.")
return
A = list_P[0]
B = list_P[1]
C = list_P[2]
D = list_P[3]
points = np.zeros((2, 2, 3))
points[0, 0, :] = A[:3]
points[1, 0, :] = B[:3]
points[0, 1, :] = C[:3]
points[1, 1, :] = D[:3]
# weights[0,0] = A[3]
# weights[1,0] = B[3]
# weights[0,1] = C[3]
# weights[1,1] = D[3]
from caid.cad_geometry import bilinear
nrb = bilinear(points=points)[0]
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def createBilinear(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
if len(list_P) != 4 :
print("You have to specify 4 markers.")
return
A = list_P[0]
B = list_P[1]
C = list_P[2]
D = list_P[3]
points = np.zeros((2,2,3))
points[0,0,:] = A[:3]
points[1,0,:] = B[:3]
points[0,1,:] = C[:3]
points[1,1,:] = D[:3]
# weights[0,0] = A[3]
# weights[1,0] = B[3]
# weights[0,1] = C[3]
# weights[1,1] = D[3]
from caid.cad_geometry import bilinear
nrb = bilinear(points=points)[0]
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def squid_square(width=4,inner_radius=6,arm_length=8,arm_width=2,fill=False):
nt = width + inner_radius # half side of the big square
import geometry
g = geometry.geometry() # create the geometry of the system
xc = [] # empty list
yc = [] # empty list
shift_y = float(arm_width-1)/2.0
for i in range(-nt,nt+1):
for j in range(-nt,nt+arm_width):
# if in the ring
yy = float(j)-shift_y # temporal y
if abs(i)>inner_radius or abs(yy)>(inner_radius+shift_y) or fill:
xc.append(float(i)) # add x coordinate
yc.append(yy) # add y coordinate
# now add right and left parts
xr = [] # empty list
yr = [] # empty list
xl = [] # empty list
yl = [] # empty list
shift_y = float(arm_width-1)/2.0
min_x = min(xc) - 1.0
max_x = max(xc) + 1.0
for i in range(arm_length):
for j in range(arm_width): # double width of the arms
xr.append(float(i)+max_x)
xl.append(-float(i)+min_x)
yr.append(float(j)-shift_y)
yl.append(float(j)-shift_y)
x = np.array(xr+xc+xl) # all the x positions
y = np.array(yr+yc+yl) # all the y positions
g.x = x # add positions in x
g.y = y # add positions in y
g.celldis = max(x) - min(x) +1.0 # distance to neighbor +1.0
g.dimensionality = 1 # 0 dimensional system
return g
def make_random(k):
vtx = random_vertex()
theta, phi = random_direction()
direct = unit_vector(theta, phi)
pts, deps = track_points(vtx, direct)
print(len(deps))
x, y, z = unzip(pts)
scatter3d_module(x, y, z, deps, k)
zero = geo.point_3d(0., 0., 0.)
#box = geo.box(714*cm, 300*cm, 510*cm, zero, "ar_cube")
module_box = geo.box(100.0 * cm, 300.0 * cm, 100 * cm, zero,
"rand" + str(k) + "_box")
geometry = geo.geometry([module_box], zero)
simul = sim.simulator(geometry)
simul.supervisor._outfile = OUT_DIR + "rand_event" + str(k) + ".root"
geom = simul.project_event(pts, deps, vtx)
simul.set_minimal()
simul.supervisor._truth.SetBinContent(1, vtx[0])
simul.supervisor._truth.SetBinContent(2, vtx[1])
simul.supervisor._truth.SetBinContent(3, vtx[2])
simul.supervisor._truth.SetBinContent(4, theta)
simul.supervisor._truth.SetBinContent(5, phi)
simul.supervisor.write()
def initialize(self, empty=False):
"""
create an empty geometry object
"""
if not empty:
from geometry import geometry
geo = geometry()
self.add_geometry(geo)
def initialize(self, empty=False):
"""
create an empty geometry object
"""
if not empty:
from geometry import geometry
geo = geometry()
self.add_geometry(geo)
def open(self, filename=None):
if filename is not None:
self.filename = filename
else:
from global_vars import CAIDWorkGroupwildcard
# Create an open file dialog
dialog = wx.FileDialog(None\
, style = wx.OPEN\
, wildcard=CAIDWorkGroupwildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
self.filename = dialog.GetPath()
# The user did not select anything
else:
print('Nothing was selected.')
# Destroy the dialog
dialog.Destroy()
from caid.cad_geometry import cad_geometry
from caid.io import XML
from geometry import geometry
io = XML()
from xml.dom.minidom import parse
doc = parse(self.filename)
rootElt = doc.documentElement
# read attributs
# get camera attributs
eye = strtoArray(rootElt.getAttribute("eye"))
self.viewer.lookAt.SetEye(eye)
center = strtoArray(rootElt.getAttribute("center"))
self.viewer.lookAt.SetCenter(center)
up = strtoArray(rootElt.getAttribute("up"))
self.viewer.lookAt.SetUp(up)
# get colors attributs
# ...
try:
self.viewer.theme.load(rootElt=rootElt)
except:
print("Theme can not be loaded. Dark theme will be used.")
self.viewer.theme.set_theme("dark")
# ...
for geoElt in rootElt.getElementsByTagName("geometry"):
geo = cad_geometry()
io.xmltogeo(geo, doc, geoElt)
_geo = geometry(geo)
_geo.load_attributs()
self.add_geometry(_geo)
self.Refresh()
# sets the temporary file for auto-save
tmp = self.filename.split('/')[-1]
basedir = self.filename.split(tmp)[0]
self.tmp_filename = basedir+"~"+tmp
def open(self, filename=None):
if filename is not None:
self.filename = filename
else:
from global_vars import CAIDWorkGroupwildcard
# Create an open file dialog
dialog = wx.FileDialog(None\
, style = wx.OPEN\
, wildcard=CAIDWorkGroupwildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
self.filename = dialog.GetPath()
# The user did not select anything
else:
print('Nothing was selected.')
# Destroy the dialog
dialog.Destroy()
from caid.cad_geometry import cad_geometry
from caid.io import XML
from geometry import geometry
io = XML()
from xml.dom.minidom import parse
doc = parse(self.filename)
rootElt = doc.documentElement
# read attributs
# get camera attributs
eye = strtoArray(rootElt.getAttribute("eye"))
self.viewer.lookAt.SetEye(eye)
center = strtoArray(rootElt.getAttribute("center"))
self.viewer.lookAt.SetCenter(center)
up = strtoArray(rootElt.getAttribute("up"))
self.viewer.lookAt.SetUp(up)
# get colors attributs
# ...
try:
self.viewer.theme.load(rootElt=rootElt)
except:
print("Theme can not be loaded. Dark theme will be used.")
self.viewer.theme.set_theme("dark")
# ...
for geoElt in rootElt.getElementsByTagName("geometry"):
geo = cad_geometry()
io.xmltogeo(geo, doc, geoElt)
_geo = geometry(geo)
_geo.load_attributs()
self.add_geometry(_geo)
self.Refresh()
# sets the temporary file for auto-save
tmp = self.filename.split('/')[-1]
basedir = self.filename.split(tmp)[0]
self.tmp_filename = basedir + "~" + tmp
def plot_dts(n, prefix='out/tireout', postfix='.dat', conf='DEFAULT'):
configactual = config[conf]
CFL = configactual.getfloat('CFL')
Cth = configactual.getfloat('Cth')
Cdiff = configactual.getfloat('Cdiff')
rstar = configactual.getfloat('rstar')
mu30 = configactual.getfloat('mu30')
m1 = configactual.getfloat('m1')
b12 = 2. * mu30 * (rstar * m1 / 6.8)**(-3)
geofile = os.path.dirname(prefix) + "/geo.dat"
print(geofile)
r, theta, alpha, across, l, delta = geo.gread(geofile)
g = geo.geometry()
g.r = r
g.theta = theta
g.alpha = alpha
g.l = l
g.delta = delta
g.across = across
g.cth = cos(theta)
dl = l[1:] - l[:-1]
dl = concatenate([dl, [dl[-1]]])
umag = b12**2 * 2.29e6 * m1
umagtar = umag * ((1. + 3. * g.cth**2) / 4. * (rstar / g.r)**6)
fname = prefix + entryname(n, ndig=5) + postfix
print(fname)
lines = loadtxt(fname, comments="#")
print(shape(lines))
r1 = lines[:, 0]
rho = lines[:, 1]
v = lines[:, 2]
u = lines[:, 3] * umagtar
print(shape(r1))
print((r1 - r).std())
csq = 4. / 3. * u / rho
dt_CFL = CFL * dl / (sqrt(csq) + abs(v))
qloss = qloss_separate(rho, v, u, g, configactual)
dt_thermal = Cth * u * g.across / qloss
dt_diff = Cdiff * dl**2 * rho * 3.
someplots(r, [dl],
ylog=True,
ytitle='$\Delta l$',
name='dl',
formatsequence=['k-'])
someplots(r, [dt_CFL, dt_thermal, dt_diff],
ylog=True,
ytitle='$\Delta t$',
name='dts',
formatsequence=['k-', 'b:', 'r--'])
def cutCurve(self):
wk = self.workGroup
try:
list_patchs = []
for item in wk.inspector.tree.selectionsItems:
patch = wk.inspector.tree.GetItemData(item)
if patch.dim > 1:
print("cut curves algorithm only works with curves")
return
list_patchs.append(patch)
if len(list_patchs) > 1:
print(("cut curves algorithm needs 1 curve, but "\
, len(list_patchs), " curves were given"))
return
from caid.utils.intersect import intersect_crv
c0 = list_patchs[0]
geo0 = cad_geometry()
geo0.append(c0)
freq = wk.viewer.cutCurveFreq
list_P = wk.viewer.CutCurvePoints[::freq]
x, y, z = list(zip(*list_P))
x = np.asarray(x)
y = np.asarray(y)
z = np.asarray(z)
from scipy import interpolate
smooth = 0.
degree = 3
tck, u = interpolate.splprep([x, y], s=smooth, k=degree)
knots = tck[0]
Px = tck[1][0]
Py = tck[1][1]
C = np.zeros((len(Px), 3))
C[:, 0] = array(Px)
C[:, 1] = array(Py)
c1 = cad_nurbs([knots], C)
geo1 = cad_geometry()
geo1.append(c1)
list_P, list_t, list_s, ierr = intersect_crv(c0, c1)
list_t = np.asarray(list_t)
list_t.sort()
axis = 0
for i, t in enumerate(list_t):
geo0.split(i, t, axis)
wk.add_geometry(geometry(geo0))
wk.Refresh()
except:
self.statusbar.SetStatusText(
'Cannot use cut Curve. Check that a patch is selected on the inspector'
)
def cutCurve(self):
wk = self.workGroup
try:
list_patchs = []
for item in wk.inspector.tree.selectionsItems:
patch = wk.inspector.tree.GetPyData(item)
if patch.dim > 1:
print("cut curves algorithm only works with curves")
return
list_patchs.append(patch)
if len(list_patchs) > 1:
print(("cut curves algorithm needs 1 curve, but ", len(list_patchs), " curves were given"))
return
from caid.utils.intersect import intersect_crv
c0 = list_patchs[0]
geo0 = cad_geometry()
geo0.append(c0)
freq = wk.viewer.cutCurveFreq
list_P = wk.viewer.CutCurvePoints[::freq]
x, y, z = list(zip(*list_P))
x = np.asarray(x)
y = np.asarray(y)
z = np.asarray(z)
from scipy import interpolate
smooth = 0.0
degree = 3
tck, u = interpolate.splprep([x, y], s=smooth, k=degree)
knots = tck[0]
Px = tck[1][0]
Py = tck[1][1]
C = np.zeros((len(Px), 3))
C[:, 0] = array(Px)
C[:, 1] = array(Py)
c1 = cad_nurbs([knots], C)
geo1 = cad_geometry()
geo1.append(c1)
list_P, list_t, list_s, ierr = intersect_crv(c0, c1)
list_t = np.asarray(list_t)
list_t.sort()
axis = 0
for i, t in enumerate(list_t):
geo0.split(i, t, axis)
wk.add_geometry(geometry(geo0))
wk.Refresh()
except:
self.statusbar.SetStatusText("Cannot use cut Curve. Check that a patch is selected on the inspector")
def get_transformation_matrix(
d_mmCIF_apo,
l_coords_alpha_apo,
d_mmCIF_holo,
l_coords_alpha_holo,
):
## structural alignment
## solution that works in all cases
## also for 2d59 and 2d5a, which have residues missing at the Nterm and Cterm, respectively
## first non-?
index1_seq_apo = next(
(i
for i, v in enumerate(d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id'])
if v != '?'))
index1_seq_holo = next((
i
for i, v in enumerate(d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id'])
if v != '?'))
## last non-?
index2_seq_apo = len(
d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id']) - next(
(i for i, v in enumerate(
reversed(d_mmCIF_apo['_pdbx_poly_seq_scheme.pdb_mon_id']))
if v != '?'))
index2_seq_holo = len(
d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id']) - next(
(i for i, v in enumerate(
reversed(d_mmCIF_holo['_pdbx_poly_seq_scheme.pdb_mon_id']))
if v != '?'))
## first common non-?
index1_coord_apo = max(0, index1_seq_holo - index1_seq_apo)
index1_coord_holo = max(0, index1_seq_apo - index1_seq_holo)
## last common non-?
index2_coord_apo = len(l_coords_alpha_apo) + min(
0, index2_seq_holo - index2_seq_apo)
index2_coord_holo = len(l_coords_alpha_holo) + min(
0, index2_seq_apo - index2_seq_holo)
l_coords_alpha_apo = l_coords_alpha_apo[index1_coord_apo:index2_coord_apo]
l_coords_alpha_holo = l_coords_alpha_holo[
index1_coord_holo:index2_coord_holo]
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(
l_coords_alpha_apo,
l_coords_alpha_holo,
)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
return tv1, rm, tv2, l_coords_alpha_apo, l_coords_alpha_holo
def get_transformation_matrix(
l_coords_alpha_apo,
l_coords_alpha_holo,
):
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(l_coords_alpha_apo,l_coords_alpha_holo,)
print 'rmsd', rmsd
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
return tv1, rm, tv2, l_coords_alpha_apo, l_coords_alpha_holo
def __init__(self): #{{{
# classtype=model.properties
# for classe in dict.keys(classtype):
# print classe
# self.__dict__[classe] = classtype[str(classe)]
self.mesh = mesh2d()
self.mask = mask()
self.geometry = geometry()
self.constants = constants()
self.smb = SMBforcing()
self.basalforcings = basalforcings()
self.materials = matice()
self.damage = damage()
self.friction = friction()
self.flowequation = flowequation()
self.timestepping = timestepping()
self.initialization = initialization()
self.rifts = rifts()
self.slr = slr()
self.debug = debug()
self.verbose = verbose()
self.settings = settings()
self.toolkits = toolkits()
self.cluster = generic()
self.balancethickness = balancethickness()
self.stressbalance = stressbalance()
self.groundingline = groundingline()
self.hydrology = hydrologyshreve()
self.masstransport = masstransport()
self.thermal = thermal()
self.steadystate = steadystate()
self.transient = transient()
self.levelset = levelset()
self.calving = calving()
self.gia = giaivins()
self.autodiff = autodiff()
self.inversion = inversion()
self.qmu = qmu()
self.amr = amr()
self.results = results()
self.outputdefinition = outputdefinition()
self.radaroverlay = radaroverlay()
self.miscellaneous = miscellaneous()
self.private = private()
def OnDrawSelectionRectangle(self, x1, y1, x2, y2):
# glClear(GL_COLOR_BUFFER_BIT)
# glBegin(GL_QUADS)
# col = self.theme.color_viewer("selection") + [self.theme.alpha]
# glColor4f(*col)
# glVertex2f(x1, y1)
# glVertex2f(x2, y1)
# glVertex2f(x2, y2)
# glVertex2f(x1, y2)
# glEnd()
points = np.asarray([[[x1,y1],[x1,y2]],[[x2,y1],[x2,y2]]])
geo_selection = geometry(bilinear(points=points))
col = self.theme.color_viewer("selection")
geo_selection.Draw(alpha=self.beta, blend=self.enableBlend, NurbsColor=col)
def OnDrawSelectionRectangle(self, x1, y1, x2, y2):
# glClear(GL_COLOR_BUFFER_BIT)
# glBegin(GL_QUADS)
# col = self.theme.color_viewer("selection") + [self.theme.alpha]
# glColor4f(*col)
# glVertex2f(x1, y1)
# glVertex2f(x2, y1)
# glVertex2f(x2, y2)
# glVertex2f(x1, y2)
# glEnd()
points = np.asarray([[[x1,y1],[x1,y2]],[[x2,y1],[x2,y2]]])
geo_selection = geometry(bilinear(points=points))
col = self.theme.color_viewer("selection")
geo_selection.Draw(alpha=self.beta, blend=self.enableBlend, NurbsColor=col)
def get_transformation_matrix(
l_coords_alpha_apo,
l_coords_alpha_holo,
):
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(
l_coords_alpha_apo,
l_coords_alpha_holo,
)
print 'rmsd', rmsd
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
return tv1, rm, tv2, l_coords_alpha_apo, l_coords_alpha_holo
def createLines(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
list_crv = []
for P,Q in zip(list_P[:-1], list_P[1:]):
points = np.zeros((2,2))
points[0,0] = P[0] ; points[0,1] = P[1]
points[1,0] = Q[0] ; points[1,1] = Q[1]
crv = linear(points = points)[0]
list_crv.append(crv)
nrb = list_crv[0]
axis = 0
for crv in list_crv[1:]:
nrb = join(nrb, crv, axis)
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def __init__(self, renderer, size):
self.geometry = geometry.geometry()
self.renderer = renderer
self.camera = camera.camera(size[0], size[1])
self.player = player.player(self.geometry)
self.mouse_screen_x = 0
self.mouse_screen_y = 0
self.mouse_x = 0
self.mouse_y = 0
self.ghost = player.player(self.geometry, True)
self.ghost_data_store = []
self.ghost_data_replay = []
self.ghost_replay_index = 0
self.font = sdl2hl.ttf.Font(resource_string(__name__, 'res/font/LiberationSans-Regular.ttf'), 24)
def squid_square(width=4,
inner_radius=6,
arm_length=8,
arm_width=2,
fill=False):
nt = width + inner_radius # half side of the big square
import geometry
g = geometry.geometry() # create the geometry of the system
xc = [] # empty list
yc = [] # empty list
shift_y = float(arm_width - 1) / 2.0
for i in range(-nt, nt + 1):
for j in range(-nt, nt + arm_width):
# if in the ring
yy = float(j) - shift_y # temporal y
if abs(i) > inner_radius or abs(yy) > (inner_radius +
shift_y) or fill:
xc.append(float(i)) # add x coordinate
yc.append(yy) # add y coordinate
# now add right and left parts
xr = [] # empty list
yr = [] # empty list
xl = [] # empty list
yl = [] # empty list
shift_y = float(arm_width - 1) / 2.0
min_x = min(xc) - 1.0
max_x = max(xc) + 1.0
for i in range(arm_length):
for j in range(arm_width): # double width of the arms
xr.append(float(i) + max_x)
xl.append(-float(i) + min_x)
yr.append(float(j) - shift_y)
yl.append(float(j) - shift_y)
x = np.array(xr + xc + xl) # all the x positions
y = np.array(yr + yc + yl) # all the y positions
g.x = x # add positions in x
g.y = y # add positions in y
g.celldis = max(x) - min(x) + 1.0 # distance to neighbor +1.0
g.dimensionality = 1 # 0 dimensional system
return g
def createLines(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
list_crv = []
for P, Q in zip(list_P[:-1], list_P[1:]):
points = np.zeros((2, 2))
points[0, 0] = P[0]
points[0, 1] = P[1]
points[1, 0] = Q[0]
points[1, 1] = Q[1]
crv = linear(points=points)[0]
list_crv.append(crv)
nrb = list_crv[0]
axis = 0
for crv in list_crv[1:]:
nrb = join(nrb, crv, axis)
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def createArc(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
if len(list_P) != 3 :
print("You have to specify 3 markers.")
return
dlg = edtTxtDialog(None, title="Edit Angle")
dlg.ShowModal()
ls_text = dlg.getValue()
try:
lr_degree = float(ls_text)
except:
lr_degree = 0.0
theta = lr_degree * pi / 180
dlg.Destroy()
A0 = list_P[0]
A1 = list_P[1]
A2 = list_P[2]
knots = [0.,0.,0.,1.,1.,1.]
C = np.zeros((3,3))
C[0,:] = A0[:3]
C[1,:] = A1[:3]
C[2,:] = A2[:3]
weights = [1.,cos(theta),1.]
nrb = cad_nurbs([knots], C, weights=weights)
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def MenuSelectionCb(self, event):
# do something
operation = self.menu_title_by_id[event.GetId()]
if operation == "New Geometry":
from geometry import geometry
geo = geometry()
wk = self.currentWorkGroup
wk.add_geometry(geo)
if operation == "Save":
self.currentWorkGroup.save()
if operation == "New Scalar Field":
F = field()
wk = self.currentWorkGroup
wk.add_field(F)
if operation == "Import Scalar Field":
filename = None
from global_vars import CAIDFieldWildcard
# Create an open file dialog
dialog = wx.FileDialog(None\
, style = wx.OPEN\
, wildcard=CAIDFieldWildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
filename = dialog.GetPath()
# The user did not select anything
else:
print('Nothing was selected.')
# Destroy the dialog
dialog.Destroy()
if filename is not None:
U = field()
U.open(filename)
wk = self.currentWorkGroup
wk.add_field(U)
wk.Refresh()
def MenuSelectionCb( self, event ):
# do something
operation = self.menu_title_by_id[ event.GetId() ]
if operation == "New Geometry":
from geometry import geometry
geo = geometry()
wk = self.currentWorkGroup
wk.add_geometry(geo)
if operation == "Save":
self.currentWorkGroup.save()
if operation == "New Scalar Field":
F = field()
wk = self.currentWorkGroup
wk.add_field(F)
if operation == "Import Scalar Field":
filename = None
from global_vars import CAIDFieldWildcard
# Create an open file dialog
dialog = wx.FileDialog(None\
, style = wx.OPEN\
, wildcard=CAIDFieldWildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
filename = dialog.GetPath()
# The user did not select anything
else:
print('Nothing was selected.')
# Destroy the dialog
dialog.Destroy()
if filename is not None:
U = field()
U.open(filename)
wk = self.currentWorkGroup
wk.add_field(U)
wk.Refresh()
def createArc(self):
wk = self.workGroup
list_P = wk.viewer.MarkerPoints
if len(list_P) != 3:
print("You have to specify 3 markers.")
return
dlg = edtTxtDialog(None, title="Edit Angle")
dlg.ShowModal()
ls_text = dlg.getValue()
try:
lr_degree = float(ls_text)
except:
lr_degree = 0.0
theta = lr_degree * pi / 180
dlg.Destroy()
A0 = list_P[0]
A1 = list_P[1]
A2 = list_P[2]
knots = [0., 0., 0., 1., 1., 1.]
C = np.zeros((3, 3))
C[0, :] = A0[:3]
C[1, :] = A1[:3]
C[2, :] = A2[:3]
weights = [1., cos(theta), 1.]
nrb = cad_nurbs([knots], C, weights=weights)
wk.viewer.CleanMarkerPoints()
geo = cad_geometry()
geo.append(nrb)
wk.add_geometry(geometry(geo))
wk.Refresh()
def OnClick(self, event):
ID = event.GetId()
if ID == self.BCK_ID:
self.parent.ShowAction(self.parent.geometryActions)
if ID == self.GO_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
_geo = cad_geometry()
for nrb in geo:
geo_t = cad_geometry()
geo_t.append(nrb)
# ... refinement
list_t = None
if self.n.sum() > 0:
list_t = []
for axis in range(0, nrb.dim):
ub = nrb.knots[axis][0]
ue = nrb.knots[axis][-1]
t = []
if self.n[axis] > 0:
t = np.linspace(ub, ue, self.n[axis] + 2)[1:-1]
list_t.append(t)
list_p = None
if self.p.sum() > 0:
list_p = []
for axis in range(0, nrb.dim):
list_p.append(
np.max(self.p[axis] - nrb.degree[axis], 0))
list_m = None
if self.m.sum() > 0:
list_m = []
for axis in range(0, nrb.dim):
list_m.append(self.m[axis])
geo_t.refine(list_t=list_t, list_p=list_p, list_m=list_m)
_geo.append(geo_t[0])
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... refine geometry")
macro_script.append("_geo = cad_geometry()")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("for nrb in geo:")
macro_script.append("\tgeo_t = cad_geometry()")
macro_script.append("\tgeo_t.append(nrb)")
str_list_t = [list(ts) for ts in list_t]
macro_script.append("\tlist_t = " + str(str_list_t))
macro_script.append("\tlist_p = " + str(list_p))
macro_script.append("\tlist_m = " + str(list_m))
macro_script.append(
"\tgeo_t.refine(list_t=list_t, list_p=list_p, list_m=list_m)"
)
macro_script.append("\t_geo.append(geo_t[0])")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
# ...
_geo.set_internal_faces(geo.internal_faces)
_geo.set_external_faces(geo.external_faces)
_geo.set_connectivity(geo.connectivity)
geo_new = geometry(_geo)
geo_newItem = wk.add_geometry(geo_new)
def main():
import os
import sys
sys.path.append('/home/people/tc/svn/Protool/trunk')
import geometry
instance_geometry = geometry.geometry()
## fd = open('clusters95.txt','r')
## lines = fd.readlines()
## fd.close()
## d_pdbs = {}
## d_clusters = {}
## for line in lines:
## cluster = int(line.split()[0])
## if cluster not in d_clusters.keys():
## d_clusters[cluster] = []
## pdb = line.split()[2]
## d_clusters[cluster] += [pdb]
## for cluster in d_clusters:
## l_pdbs = d_clusters[cluster]
## if '2LZM:A' in l_pdbs:
## break
pdb1 = '2lzt'
## l_pdbs = ['189L:A', '1C69:A', '1C6A:A', '1C6B:A', '1D9W:A', '1DYA:A', '1DYB:A', '1DYC:A', '1DYD:A', '1DYE:A', '1DYF:A', '1DYG:A', '1L00:A', '1L02:A', '1L03:A', '1L04:A', '1L05:A', '1L06:A', '1L07:A', '1L08:A', '1L09:A', '1L10:A', '1L11:A', '1L12:A', '1L13:A', '1L14:A', '1L15:A', '1L16:A', '1L17:A', '1L18:A', '1L19:A', '1L20:A', '1L21:A', '1L22:A', '1L23:A', '1L24:A', '1L25:A', '1L26:A', '1L27:A', '1L28:A', '1L29:A', '1L30:A', '1L31:A', '1L32:A', '1L33:A', '1L34:A', '1L37:A', '1L38:A', '1L42:A', '1L43:A', '1L44:A', '1L45:A', '1L46:A', '1L47:A', '1L48:A', '1L52:A', '1L53:A', '1L56:A', '1L57:A', '1L58:A', '1L60:A', '1L69:A', '1L70:A', '1L71:A', '1L96:A', '1L97:A', '1L97:B', '1L98:A', '1L99:A', '1LYD:A', '1T6H:A', '223L:A', '225L:A', '226L:A', '256L:A', '2LZM:A', '3LZM:A', '4LZM:A', '5LZM:A', '6LZM:A', '7LZM:A']
## l_pdbs.remove('%s:A' %(pdb1.upper()))
## l_pdbs.sort()
l_pdbs = [
'1sfg:A',
'1ja7:A',
'1h6m:A',
]
l_pdbs2 = [
## antibody
## '2eiz','2eks','2yss','1a2y','1bql','1bvk','1c08','1fdl','1g7h','1g7i',
## '1g7j','1g7l','1g7m',
'1mel',
'1nbz',
'1yqv',
'1zvh',
## MODRES
'132l',
'1at5',
'1at6',
## inhibitor
'1gpq',
'1uuz',
## deletion
'1uia',
'1uib',
## glycosylated
'2b5z',
## NMR
'1e8l',
## multiple models
'1hc0',
'2d6b',
## different length
'1lsg',
]
l_pdbs_2lzm = [
## modified residue
'1t6h',
## beta-mercapto-ethanol
'1l97',
]
d_coordinates = {}
d_coordinates[pdb1], l_coordinates1 = parse_coordinates(pdb1, 'A')
max_rmsd = [0, 0]
for i in range(len(l_pdbs)):
pdb = l_pdbs[i][:4].lower()
chain = l_pdbs[i][-1]
if pdb in l_pdbs_2lzm:
continue
## if i+1 < int(sys.argv[1]):
## continue
d_coordinates[pdb], l_coordinates2 = parse_coordinates(pdb, chain)
if len(l_coordinates1) == 164 and len(l_coordinates2) in [
162,
163,
]:
rmsd = instance_geometry.superpose(
l_coordinates1[:len(l_coordinates2)], l_coordinates2)
elif len(l_coordinates1) != len(l_coordinates2):
print pdb, chain, len(l_coordinates1), len(l_coordinates2)
stop
else:
rmsd = instance_geometry.superpose(l_coordinates1, l_coordinates2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
print pdb, chain, i + 1, len(l_pdbs), rmsd
if rmsd > max_rmsd[1]:
max_rmsd = [pdb, rmsd]
print max_rmsd
return
from geometry import geometry nom, denom = map(int, input().split()) n = int(input()) prec = 3 print(round(geometry(n, nom / denom), prec))
def main(
self, jobid, lines, atoms_hessian = ['CA'], frames = 51,
cutoff_distance = 10.,
path_html = None, path_python = None, verbose = False, paralleldir = '',
biomolecule = None, chains = [], model = None,
winsize = 1, stepsize = 1,
):
'''
Use first model if no model specified by user.
chain(s): Y, biomolecule: Y; parse chains specified by user and apply transformation
chain(s): Y, biomolecule: N; parse chains specified by user but don't apply transformation
chain(s): N, biomolecule: Y; parse chains of biomolecule and apply transformation
chain(s): N, biomolecule: N; parse chains of first biomolecule and apply transformation
'''
import os, Numeric, goodvibes_core
if stepsize not in [1,winsize]:
raise 'stepsize must be 1 or equal to winsize'
results = []
## parse pdb
(
d_REMARK350,
d_primary, ## i.e. SEQRES, MODRES
d_secondary, ## i.e. HELIX, SHEET
d_coordinates, ## i.e. ATOM, HETATM, TER, MODEL, ENDMDL
) = self.parse_pdb(lines, chains, model)
## assume multimeric biological unit if chains not specified by user
if chains == []:
chains = d_coordinates['chains'].keys()
chains.sort()
##
## d_coordinates to l_coordinates
##
l_coordinates = []
for chain in chains:
## assuming sequential numbering of residues
res_nos = d_coordinates['chains'][chain]['residues'].keys()
res_nos.sort()
for res_no in res_nos:
for iCode in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'].keys():
altloc = min(d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'].keys())
for atom_name in d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms'].keys():
if atom_name in atoms_hessian:
coordinate = d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms'][atom_name]['coordinate']
d_coordinates['chains'][chain]['residues'][res_no]['iCodes'][iCode]['altlocs'][altloc]['atoms'][atom_name]['hessian'] = True
l_coordinates += [coordinate]
## cluster coordinates
l_coordinates = [sum(l_coordinates[i:i+winsize])/winsize for i in range(0,len(l_coordinates),winsize)]
N = len(l_coordinates)
## calculate intra-residue distances
matrix_distance_residue_intra = self.distance_residue_intra(l_coordinates)
## for the non-disrupted structure: calculate and visualize eigenvectors
matrix_hessian = self.hessian_calculation(l_coordinates, float(cutoff_distance), verbose)
eigenvectors_nonperturbed, eigenvalues_nonperturbed, eigenvectors_combined_nonperturbed = self.eigenv_calccomb(matrix_hessian, jobid, verbose)
import math
d_energies = {}
d_factors = {}
## read pdb2
pdb2 = '2lzm'
chains2 = ['A']
fd = open('/oxygenase_local/data/pdb/%s/pdb%s.ent' %(pdb2[1:3],pdb2,),'r')
lines2 = fd.readlines()
fd.close()
## parse pdb2
(
d_REMARK350_2,
d_primary2, ## i.e. SEQRES, MODRES
d_secondary2, ## i.e. HELIX, SHEET
d_coordinates2, ## i.e. ATOM, HETATM, TER, MODEL, ENDMDL
d_ligands2,
) = goodvibes_core.parse_pdb(lines2, chains2)
N2, d_hessian2, l_coordinates2 = goodvibes_core.parse_dictionary_of_coordinates(d_coordinates2, chains2, atoms_hessian)
## rotate coordinates2
import sys, numpy
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(l_coordinates[:-2],l_coordinates2)
print 'rmsd', rmsd
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
for i in range(len(l_coordinates2)):
coord = l_coordinates2[i]
tcoord = numpy.dot(coord-tv1,rm)+tv2
l_coordinates2[i] = tcoord
## calculate coordinates2 energies
V = 0
E = 0
l_E = []
maxi = [0,'N/A',]
mini = 9999
lines_rasmol_colors = []
for i in range(0,len(l_coordinates2)*3,3):
res_index1 = i/3
xa1 = l_coordinates[res_index1][0]
ya1 = l_coordinates[res_index1][1]
za1 = l_coordinates[res_index1][2]
xa2 = l_coordinates2[res_index1][0]
ya2 = l_coordinates2[res_index1][1]
za2 = l_coordinates2[res_index1][2]
E = 0
for j in range(0,len(l_coordinates2)*3,3):
if i == j:
continue
res_index2 = j/3
xb1 = l_coordinates[res_index2][0]
yb1 = l_coordinates[res_index2][1]
zb1 = l_coordinates[res_index2][2]
xb2 = l_coordinates2[res_index2][0]
yb2 = l_coordinates2[res_index2][1]
zb2 = l_coordinates2[res_index2][2]
kx = matrix_hessian[i+0][j+0]
ky = matrix_hessian[i+1][j+1]
kz = matrix_hessian[i+2][j+2]
## k = math.sqrt(kx**2+ky**2+kz**2)
## E = .5*kx*(vx**2)+.5*ky*(vy**2)+.5*kz*(vz**2)
## E -= .5*kx*((vxb-vxa)**2)+.5*ky*((vyb-vya)**2)+.5*kz*((vzb-vza)**2)
E -= .5*kx*(((xb2-xa2)-(xb1-xa1))**2)+.5*ky*(((yb2-ya2)-(yb1-ya1))**2)+.5*kz*(((zb2-za2)-(zb1-za1))**2)
if E < mini:
mini = E
if E > maxi[0]:
maxi = [E,res_index1]
l_E += [E/0.39]
index = E/0.39
h = 159.+80*index/100.
s = 240.
l = 120.+120.*(50-abs(index-50))/50.
r,g,b = self.hsl2rgb(h,s,l,)
lines_rasmol_colors += [
'select %i\n' %(res_index1+1),
'color [%i,%i,%i]\n' %(
r, g, b,
)
]
lines_pdb2_rotated = []
## rotate pdb
for line in lines2:
record = line[:6].strip()
if record == 'HETATM':
continue
elif record != 'ATOM':
lines_pdb2_rotated += [line]
continue
if line[21] not in chains2:
continue
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coordinate = numpy.array([x,y,z,])
coordinate = numpy.dot(coordinate-tv1,rm)+tv2
bfactor = float(line[60:66])
line_rotated = '%s%8.3f%8.3f%8.3f%s%6.2f%s' %(
line[:30],
coordinate[0],coordinate[1],coordinate[2],
line[54:60],bfactor,line[66:]
)
lines_pdb2_rotated += [line_rotated]
fd = open('%s_rotated.pdb' %(pdb2),'w')
fd.writelines(lines_pdb2_rotated)
fd.close()
## write rasmol script
lines = [
'rasmol -nodisplay %s_rotated.pdb << EOF\n' %(pdb2),
'cartoon\n',
'wireframe 0\n',
## 'ribbons\n',
## 'color temperature\n',
]
lines += lines_rasmol_colors
lines += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write 150l.ppm\n',
'exit\n',
]
## write rasmol script to file
fd = open('rasmol.src','w')
fd.writelines(lines)
fd.close()
## execute rasmol script
os.system('source rasmol.src > rasmol.log')
## convert rasmol output
os.system('convert 150l.ppm 150l.gif')
## clean up
os.remove('150l.ppm')
os.remove('rasmol.log')
## os.remove('rasmol.src')
print l_E
print 'minmax', mini,maxi
## self.morph(
## eigenvectors_nonperturbed, frames, chains, d_coordinates, atoms_hessian, matrix_hessian, jobid,
## d_energies,d_factors,
## )
return results
def default_geo():
module_box = geo.box(100.0 * cm, 300.0 * cm, 100 * cm)
geometry = geo.geometry([module_box], zero)
return geometry
def main():
set_pdbs = exclude_include()
l_pdbs_remove = [
'4a3h','2wf5','1arl','1ee3', ## incorrect _struct_ref_seq.pdbx_db_accession
'1uyd','1uye','1uyf','2byh','2byi', ## remediation _struct_ref_seq_dif
'2xdu','3dn8','3dna','1ps3','1ouf','1l35','2eun','1rtc','1zon', ## _struct_ref_seq_dif missing
'1pwl','1pwm','2fz8','2fz9', ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
]
set_pdbs.remove('1f92') ## remediation _struct_ref_seq_dif incorrect residue number
set_pdbs.remove('2f6f') ## remediation _pdbx_poly_seq_scheme.auth_mon_id wrong
set_pdbs.remove('3a5j') ## remediation _struct_ref_seq_dif.db_mon_id is ? but should be MET
set_pdbs.remove('2rhx') ## remediation _struct_ref_seq_dif.db_mon_id is ? but should be SER
set_pdbs.remove('2fzb') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('2fzd') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('3dn5') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('1x96') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('1x97') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('1x98') ## remediation incorrect _struct_ref.pdbx_seq_one_letter_code
set_pdbs.remove('1z3n') ## GenBank DBref - not an error...
set_pdbs.remove('1z8a') ## GenBank DBref - not an error...
set_pdbs.remove('1z89') ## GenBank DBref - not an error...
set_pdbs.remove('2pf8') ## stupid use of alt_ids (C for highest occupancy and only altloc)
set_pdbs.remove('2pyr') ## stupid use of alt_ids (G and R)
set_pdbs.remove('3pdn') ## stupid use of alt_ids (B and C)
set_pdbs.remove('2v4c') ## alt_id B used for 100% occupancy atoms
set_pdbs.remove('1jxt') ## weird alt_id microheterogeneity...
set_pdbs.remove('1jxu') ## weird alt_id microheterogeneity...
set_pdbs.remove('1jxw') ## weird alt_id microheterogeneity...
set_pdbs.remove('1jxx') ## weird alt_id microheterogeneity...
set_pdbs.remove('1jxy') ## weird alt_id microheterogeneity...
## set_pdbs.remove('1ac4') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)...
## set_pdbs.remove('1ac8') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)...
## set_pdbs.remove('1aeb') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)...
## set_pdbs.remove('2rbt') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)... UNP A7A026, TAX 307796, STRAIN YJM789
## set_pdbs.remove('2rbu') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)... UNP A7A026, TAX 307796, STRAIN YJM789
## set_pdbs.remove('2rbv') ## multiple strains and taxonomy ids but all same organism (S. cerevisiae)... UNP A7A026, TAX 307796, STRAIN YJM789
for pdb in l_pdbs_remove:
set_pdbs.remove(pdb)
fd = open('%s/bc-100.out' %(path_mmCIF),'r')
lines = fd.readlines()
fd.close()
for i_line in range(len(lines)):
cluster = i_line
if cluster < 4816:
continue
## if cluster not in [5,]:
## continue
line = lines[i_line]
l_pdbs = line.lower().split()
l_pdbs.sort()
for i_pdb in range(len(l_pdbs)):
l_pdbs[i_pdb] = l_pdbs[i_pdb][:4]
for i_pdb1 in range(0,len(l_pdbs)-1):
pdb1 = l_pdbs[i_pdb1]
## if pdb1 != '1t49': ## tmp!!!
## continue
if not pdb1 in set_pdbs:
continue
print pdb1
stop
d_mmCIF1 = parse_mmCIF.main(pdb1,)
bool_monomeric = check_monomeric(d_mmCIF1)
if bool_monomeric == False:
if i_pdb1 == 0:
break
else:
continue
bool_remediation_modres = check_modres(d_mmCIF1,pdb1,)
if bool_remediation_modres == True:
continue
if '_struct_ref_seq_dif.details' in d_mmCIF1.keys():
if 'DELETION' in d_mmCIF1['_struct_ref_seq_dif.details']:
continue
for i_entity in range(len(d_mmCIF1['_entity.id'])):
if d_mmCIF1['_entity.type'][i_entity] == 'polymer':
if int(d_mmCIF1['_entity.pdbx_number_of_molecules'][i_entity]) != 1:
print d_mmCIF1['_entity.pdbx_number_of_molecules']
print pdb1, cluster
stop
SG1 = d_mmCIF1['_symmetry.space_group_name_H-M']
for i_pdb2 in range(i_pdb1+1,len(l_pdbs)):
pdb2 = l_pdbs[i_pdb2]
## if pdb2 != '2pf8': ## tmp!!!
## continue
## if pdb1 != '3fui' or pdb2 != '3fuj':
## continue
if not pdb2 in set_pdbs:
continue
d_mmCIF2 = parse_mmCIF.main(pdb2,)
bool_monomeric = check_monomeric(d_mmCIF2)
if bool_monomeric == False:
continue
bool_remediation_modres = check_modres(d_mmCIF2,pdb2,)
if bool_remediation_modres == True:
continue
if '_struct_ref_seq_dif.seq_num' in d_mmCIF2.keys():
if 'DELETION' in d_mmCIF2['_struct_ref_seq_dif.details']:
continue
## biounit monomeric?
for i_entity in range(len(d_mmCIF2['_entity.id'])):
if d_mmCIF2['_entity.type'][i_entity] == 'polymer':
if int(d_mmCIF2['_entity.pdbx_number_of_molecules'][i_entity]) != 1:
continue
SG2 = d_mmCIF2['_symmetry.space_group_name_H-M']
if SG1 != SG2:
continue
## parse coordinates again after being shortened in previous loop
try:
d_coords1, l_coords_alpha1 = mmCIF2coords.main(pdb1, d_mmCIF1)
except:
fd = open('remediation_atom_site.label_alt_id.txt','a')
fd.write('%s\n' %(pdb1,))
fd.close()
try:
d_coords2, l_coords_alpha2 = mmCIF2coords.main(pdb2, d_mmCIF2)
except:
fd = open('remediation_atom_site.label_alt_id.txt','a')
fd.write('%s\n' %(pdb2,))
fd.close()
## align sequences/coordinates
try:
l_coords_alpha1, l_coords_alpha2 = create_apo_holo_dataset.sequential_alignment_of_coordinates(
l_coords_alpha1, l_coords_alpha2,
d_mmCIF1, d_mmCIF2,
pdb1, pdb2,
)
except:
fd = open('remediation_struct_ref_seq_dif.txt','a')
fd.write(
'%s %s %s %s\n' %(
pdb1,pdb2,
d_mmCIF1['_struct_ref_seq.pdbx_db_accession'],
d_mmCIF2['_struct_ref_seq.pdbx_db_accession'],
)
)
fd.close()
continue
if len(l_coords_alpha1) != len(l_coords_alpha2):
print d_mmCIF1['_pdbx_poly_seq_scheme.pdb_mon_id']
print d_mmCIF2['_pdbx_poly_seq_scheme.pdb_mon_id']
print 'coords', len(l_coords_alpha1), len(l_coords_alpha2)
print 'seq', len(d_mmCIF1['_pdbx_poly_seq_scheme.pdb_mon_id'])
print 'seq', len(d_mmCIF2['_pdbx_poly_seq_scheme.pdb_mon_id'])
print pdb1, pdb2
d_coords1, l_coords_alpha1 = mmCIF2coords.main(pdb1, d_mmCIF1)
d_coords1, l_coords_alpha2 = mmCIF2coords.main(pdb1, d_mmCIF2)
print len(l_coords_alpha1), len(l_coords_alpha2)
stop
continue
##
## align structure 1 and 2
##
instance_geometry = geometry.geometry()
rmsd = instance_geometry.superpose(l_coords_alpha1,l_coords_alpha2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
## structural alignment
for i_coord in range(len(l_coords_alpha2)):
l_coords_alpha2[i_coord] = numpy.dot(l_coords_alpha2[i_coord]-tv1,rm)+tv2
##
## vector from structure 1 to 2
##
vector = []
for i in range(len(l_coords_alpha1)):
vector += [
l_coords_alpha1[i][0]-l_coords_alpha2[i][0],
l_coords_alpha1[i][1]-l_coords_alpha2[i][1],
l_coords_alpha1[i][2]-l_coords_alpha2[i][2],
]
vector = numpy.array(vector)
##
## calculate normal modes of structure 1
##
cutoff = 10
try:
matrix_hessian1 = NMA.hessian_calculation(l_coords_alpha1, cutoff, verbose = False)
eigenvectors1, eigenvalues1 = NMA.diagonalize_hessian(matrix_hessian1, verbose = False)
matrix_hessian2 = NMA.hessian_calculation(l_coords_alpha2, cutoff, verbose = False)
eigenvectors2, eigenvalues2 = NMA.diagonalize_hessian(matrix_hessian2, verbose = False)
except:
continue
##
## calculate overlap between normal modes and difference vector
##
eigenvector1 = eigenvectors1[6]
eigenvector2 = eigenvectors2[6]
overlap1 = calc_overlap(eigenvector1,vector)
overlap2 = calc_overlap(eigenvector2,vector)
overlap3a = calc_overlap(eigenvector1,eigenvector2)
overlap3b = calc_overlap(eigenvectors1[6],eigenvectors2[7])
overlap3c = calc_overlap(eigenvectors1[7],eigenvectors2[6])
overlap3 = max(overlap3a,overlap3b,overlap3c)
fd = open('rmsd_v_overlap2/cluster%i.txt' %(i_line),'a')
fd.write('%s %s\n' %(rmsd,overlap1))
fd.close()
fd = open('rmsd_v_overlap2/cluster%i.txt' %(i_line),'a')
fd.write('%s %s\n' %(rmsd,overlap2))
fd.close()
fd = open('rmsd_v_overlap2/cluster%i_ev_v_ev.txt' %(i_line),'a')
fd.write('%s %s\n' %(rmsd,overlap3a))
fd.close()
fd = open('rmsd_v_overlap2/cluster%i_ev_v_ev_max.txt' %(i_line),'a')
fd.write('%s %s\n' %(rmsd,overlap3))
fd.close()
print pdb1, pdb2, 'cluster', i_line, 'size', len(l_pdbs),
print 'overlap', '%4.2f' %(round(overlap1,2)), '%4.2f' %(round(overlap2,2)), '%4.2f' %(round(overlap3,2)), 'rmsd', '%4.2f' %(round(rmsd,2))
return
surfaceloop | volume | physicalsurface | physicalvolume | comment \
| skip1
grammar = OneOrMore(command) + StringEnd()
try:
tokens = grammar.parseFile(filename)
except ParseException, err:
print err.line
print " " * (err.column - 1) + "^"
print err
raise err
lineloops = {}
surfaceloops = {}
g = geom.geometry()
for x in tokens:
if x[0] == "Point":
g.addpoint(int(x[1]),
[float(x[2][0]),
float(x[2][1]),
float(x[2][2])])
elif x[0] == "Line":
assert len(x[2]) == 2
g.addline(int(x[1]), [int(x[2][0]), int(x[2][1])])
elif x[0] == "Circle":
assert len(x[2]) == 3
g.addline(int(x[1]), [int(x[2][0]), int(x[2][2])])
#g.add1(geom.circle(int(x[1]),int(x[2][0]),int(x[2][1]),
# int(x[2][2])))
elif x[0] == "Line Loop":
def main():
import os
import sys
sys.path.append('/home/people/tc/svn/Protool/trunk')
import geometry
instance_geometry = geometry.geometry()
## fd = open('clusters95.txt','r')
## lines = fd.readlines()
## fd.close()
## d_pdbs = {}
## d_clusters = {}
## for line in lines:
## cluster = int(line.split()[0])
## if cluster not in d_clusters.keys():
## d_clusters[cluster] = []
## pdb = line.split()[2]
## d_clusters[cluster] += [pdb]
## for cluster in d_clusters:
## l_pdbs = d_clusters[cluster]
## if '2LZM:A' in l_pdbs:
## break
pdb1 = '2lzt'
## l_pdbs = ['189L:A', '1C69:A', '1C6A:A', '1C6B:A', '1D9W:A', '1DYA:A', '1DYB:A', '1DYC:A', '1DYD:A', '1DYE:A', '1DYF:A', '1DYG:A', '1L00:A', '1L02:A', '1L03:A', '1L04:A', '1L05:A', '1L06:A', '1L07:A', '1L08:A', '1L09:A', '1L10:A', '1L11:A', '1L12:A', '1L13:A', '1L14:A', '1L15:A', '1L16:A', '1L17:A', '1L18:A', '1L19:A', '1L20:A', '1L21:A', '1L22:A', '1L23:A', '1L24:A', '1L25:A', '1L26:A', '1L27:A', '1L28:A', '1L29:A', '1L30:A', '1L31:A', '1L32:A', '1L33:A', '1L34:A', '1L37:A', '1L38:A', '1L42:A', '1L43:A', '1L44:A', '1L45:A', '1L46:A', '1L47:A', '1L48:A', '1L52:A', '1L53:A', '1L56:A', '1L57:A', '1L58:A', '1L60:A', '1L69:A', '1L70:A', '1L71:A', '1L96:A', '1L97:A', '1L97:B', '1L98:A', '1L99:A', '1LYD:A', '1T6H:A', '223L:A', '225L:A', '226L:A', '256L:A', '2LZM:A', '3LZM:A', '4LZM:A', '5LZM:A', '6LZM:A', '7LZM:A']
## l_pdbs.remove('%s:A' %(pdb1.upper()))
## l_pdbs.sort()
l_pdbs = ['1sfg:A','1ja7:A','1h6m:A',]
l_pdbs2 = [
## antibody
## '2eiz','2eks','2yss','1a2y','1bql','1bvk','1c08','1fdl','1g7h','1g7i',
## '1g7j','1g7l','1g7m',
'1mel','1nbz','1yqv','1zvh',
## MODRES
'132l','1at5','1at6',
## inhibitor
'1gpq','1uuz',
## deletion
'1uia','1uib',
## glycosylated
'2b5z',
## NMR
'1e8l',
## multiple models
'1hc0','2d6b',
## different length
'1lsg',
]
l_pdbs_2lzm = [
## modified residue
'1t6h',
## beta-mercapto-ethanol
'1l97',
]
d_coordinates = {}
d_coordinates[pdb1],l_coordinates1 = parse_coordinates(pdb1,'A')
max_rmsd = [0,0]
for i in range(len(l_pdbs)):
pdb = l_pdbs[i][:4].lower()
chain = l_pdbs[i][-1]
if pdb in l_pdbs_2lzm:
continue
## if i+1 < int(sys.argv[1]):
## continue
d_coordinates[pdb],l_coordinates2 = parse_coordinates(pdb,chain)
if len(l_coordinates1) == 164 and len(l_coordinates2) in [162,163,]:
rmsd = instance_geometry.superpose(l_coordinates1[:len(l_coordinates2)],l_coordinates2)
elif len(l_coordinates1) != len(l_coordinates2):
print pdb, chain, len(l_coordinates1), len(l_coordinates2)
stop
else:
rmsd = instance_geometry.superpose(l_coordinates1,l_coordinates2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
print pdb, chain, i+1, len(l_pdbs), rmsd
if rmsd > max_rmsd[1]:
max_rmsd = [pdb,rmsd]
print max_rmsd
return
def main(
pdb1,
pdb2,
chains1_align,
chains2_align,
):
chains1_apply = chains1_align
chains2_apply = chains2_align
import os, sys, math
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
domain_range = range(0, 9999)
os.system('cp /data/pdb-v3.2/%s/pdb%s.ent %s.pdb' % (
pdb1[1:3],
pdb1,
pdb1,
))
os.system('cp /data/pdb-v3.2/%s/pdb%s.ent %s.pdb' % (
pdb2[1:3],
pdb2,
pdb2,
))
ss_range1, l_missing1, seqres1, l_modres = parse_header(
pdb1,
chains1_align,
)
ss_range2, l_missing2, seqres2, l_modres = parse_header(
pdb2,
chains2_align,
)
ss_range = list(set(ss_range1) & set(ss_range2))
l_missing = list(set(l_missing1) | set(l_missing2))
if len(seqres1) != len(seqres2):
d_replace = {
'TPO': 'THR',
'PTR': 'TYR',
## 'SER':'CYS', ## 1tde v 1f6m
}
for i in range(len(seqres1)):
if seqres1[i] in d_replace.keys():
seqres1[i] = d_replace[seqres1[i]]
for i in range(len(seqres2)):
if seqres2[i] in d_replace.keys():
seqres2[i] = d_replace[seqres2[i]]
if not (''.join(seqres1) in ''.join(seqres2)
or ''.join(seqres2) in ''.join(seqres1)):
import sys
sys.path.append('/home/people/tc/svn/EAT_DB/')
import sequence_alignment
d_res = {
'ALA': 'A',
'CYS': 'C',
'ASP': 'D',
'GLU': 'E',
'PHE': 'F',
'GLY': 'G',
'HIS': 'H',
'ILE': 'I',
'LYS': 'K',
'LEU': 'L',
'MET': 'M',
'ASN': 'N',
'PRO': 'P',
'GLN': 'Q',
'ARG': 'R',
'SER': 'S',
'THR': 'T',
'VAL': 'V',
'TRP': 'W',
'TYR': 'Y',
}
seq1 = ''
for res in seqres1:
seq1 += d_res[res]
seq2 = ''
for res in seqres2:
seq2 += d_res[res]
instance = sequence_alignment.NW(seq1, seq2)
s1, s2 = instance.Align(verbose=False)[:2]
l1 = len(s1) - len(s1.lstrip('-'))
l2 = len(s2) - len(s2.lstrip('-'))
r1 = len(s1) - len(s1.rstrip('-'))
r2 = len(s2) - len(s2.rstrip('-'))
print seqres1
print seqres2
print len(seqres1)
print len(seqres2)
print pdb1, pdb2
print l1, l2, r1, r2
print seqres2[l1:len(seqres2) - r1]
print seqres1[l2:len(seqres1) - r2]
else:
s1 = ''.join(seqres1)
s2 = ''.join(seqres2)
if s1 in s2:
seqres2 = seqres2[s2.index(s1) / 3:]
else:
seqres1 = seqres1[s1.index(s2) / 3:]
if len(seqres1) != len(seqres2):
print len(seqres1), len(seqres2)
stop
l_coordinates1 = parse_coordinates(
pdb1,
chains1_align,
domain_range,
ss_range,
l_missing,
)
l_coordinates2 = parse_coordinates(
pdb2,
chains2_align,
domain_range,
ss_range,
l_missing,
)
## l_coordinates1 = l_coordinates1[l2:len(l_coordinates1)-r2]
## l_coordinates2 = l_coordinates2[l1:len(l_coordinates2)-r1]
if len(l_coordinates1) == 0 or len(l_coordinates2) == 0:
stop
if len(l_coordinates1) != len(l_coordinates2):
print len(l_coordinates1)
print len(l_coordinates2)
stop
rmsd = instance_geometry.superpose(l_coordinates1, l_coordinates2)
print pdb1, pdb2
print 'rmsd', round(rmsd, 1)
print 'residues', len(seqres1), len(seqres2)
print 'coordinates', len(l_coordinates1)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
lines1 = apply_transformation_matrix(
pdb1,
chains1_apply,
l_modres,
[0, 0, 0],
[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
[0, 0, 0],
)
lines2 = apply_transformation_matrix(
pdb2,
chains2_apply,
l_modres,
tv1,
rm,
tv2,
)
fd = open('rotated_%s%s.pdb' % (
pdb1,
pdb2,
), 'w')
fd.writelines(lines1 + lines2)
fd.close()
l_coordinates1 = parse_coordinates(
'rotated_' + pdb1,
chains1_apply,
range(-9999, 9999),
ss_range,
l_missing,
)
l_coordinates2 = parse_coordinates(
'rotated_' + pdb2,
chains2_apply,
range(-9999, 9999),
ss_range,
l_missing,
)
SUM = 0.
n = len(l_coordinates1)
for i in range(n):
SUM += sum((l_coordinates1[i] - l_coordinates2[i])**2)
RMSD = math.sqrt(SUM / n)
print 'RMSD all atoms', RMSD
return RMSD, l_coordinates1, l_coordinates2
def main():
import os, sys, math
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
## ## lactoferrin
## pdb1 = '1lfg'
## pdb2 = '1lfh'
## domain_range = range(1,88+1)+range(253,333+1)
## chain = 'A'
## ## trp repressor
## pdb1 = '1wrp'
## pdb2 = '2oz9' ## 2wrp
## pdb2 = '1zt9'
## domain_range = range(1,999+1)
## chain1 = 'R'
## chain2 = 'R'
## chain2 = 'A'
## exclude_chain = ''
## ## luciferase
## pdb1 = '1ba3'
## pdb2 = '1lci'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = ''
## ## G3P DH
## pdb1 = '1gd1'
## pdb2 = '2gd1'
## domain_range = range(1,999+1)
## chain1 = 'O'
## chain2 = 'O'
## exclude_chain = ''
## ## hexokinase
## pdb1 = '1hkg'
## pdb2 = '2yhx'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = ''
## ## adk
## pdb1 = '1ake'
## pdb2 = '4ake'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = 'B'
## ## t4l
## pdb1 = '2lzm'
## pdb2 = '150l'
#### domain_range = range(15,59+1)
#### domain_range = range(60,80+1)
## domain_range = range(81,162+1)
## chain1 = 'A'
## chain2 = 'D'
## exclude_chain = 'B'
l_input = [
## ##
## {'pdb1':'1ipd','pdb2':'1osj','chain1':'A','chain2':'A','range':range(1,98+1)+range(253,345+1)},
## {'pdb1':'1ipd','pdb2':'1osj','chain1':'A','chain2':'A','range':range(99,108+1)+range(109,252+1)},
###### shears
## ## aspartate amino transferase
## {'pdb1':'9aat','pdb2':'1ama','chain1':'A','chain2':'A','range':range(15,36+1)+range(349,410+1)},
## {'pdb1':'9aat','pdb2':'1ama','chain1':'A','chain2':'A','range':range(50,312+1)},
## alcohol dehydrogenase
{'pdb1':'6adh','pdb2':'8adh1','chain1':'A','chain2':'A','range':range(1,174+1)+range(322,374+1)},
{'pdb1':'6adh','pdb2':'8adh2','chain1':'A','chain2':'A','range':range(193,317+1)},
## ## citrate synthase
## {'pdb1':'1cts','pdb2':'4cts','chain1':'A','chain2':'A','range':range(1,276+1)+range(386,999+1)},
###### hinges
## ## atpsulf
## {'pdb1':'1i2d','pdb2':'1m8p','chain1':'A','chain2':'A','range':range(1,389+1)},
## ## dnak (different spacegroups)
## {'pdb1':'1dkx','pdb2':'1dky','chain1':'A','chain2':'A','range':range(389,509+1)},
## ## dnak (different spacegroups)
## {'pdb1':'1ddt','pdb2':'1mdt','chain1':'A','chain2':'A','range':range(1,376+1)},
## ## ecpdpbp
## {'pdb1':'1dpp','pdb2':'1dpe','chain1':'A','chain2':'A','range':range(1,260+1)+range(479,999+1)},
## ## ef2
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(1,478+1)}, ## large
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(479,560+1)}, ## independent
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(561,9999+1)}, ## small
## ## febp
## {'pdb1':'1d9v','pdb2':'1mrp','chain1':'A','chain2':'A','range':range(109,227+1)+range(292,309+1)},
## {'pdb1':'1d9v','pdb2':'1mrp','chain1':'A','chain2':'A','range':range(1,96+1)+range(228,262+1)},
## ## folylpolyglutamate synthetase
## {'pdb1':'1jbv','pdb2':'1jbw','chain1':'A','chain2':'A','range':range(1,295+1)},
## {'pdb1':'1jbv','pdb2':'1jbw','chain1':'A','chain2':'A','range':range(296,386+1)},
## ## glucose ABC transporter ATPase subunit (different spacegroups)
## {'pdb1':'1oxs','pdb2':'1oxu','chain1':'C','chain2':'C','range':range(1,209+1)},
## {'pdb1':'1oxs','pdb2':'1oxu','chain1':'C','chain2':'C','range':range(244,999+1)},
## ## groel domain
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(1,137+1)+range(410,999+1)},
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(192,374+1)},
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(138,190+1)+range(375,409+1)},
## ## lao bp
## {'pdb1':'2lao','pdb2':'1laf','chain1':'A','chain2':'E','range':range(1,90+1)+range(192,238+1)},
## {'pdb1':'2lao','pdb2':'1laf','chain1':'A','chain2':'E','range':range(91,191+1)},
## ## t4l
## {'pdb1':'1l96','pdb2':'1l97','chain1':'A','chain2':'A','range':range(13,59+1)},
## {'pdb1':'1l96','pdb2':'1l97','chain1':'A','chain2':'A','range':range(81,164+1)},
## ## maltodextrin bp
## {'pdb1':'1omp','pdb2':'3mbp','chain1':'A','chain2':'A','range':range(1,104+1)+range(268,313+1)},
## {'pdb1':'1omp','pdb2':'3mbp','chain1':'A','chain2':'A','range':range(113,258+1)+range(314,370+1)},
## ## mRNA capping enzyme
## {'pdb1':'1ckm','pdb2':'1ckm','chain1':'A','chain2':'B','range':range(1,237+1)+range(319,327+1)},
## {'pdb1':'1ckm','pdb2':'1ckm','chain1':'A','chain2':'B','range':range(241,303+1)},
## ## mura
## {'pdb1':'1ejd','pdb2':'1a2n','chain1':'A','chain2':'A','range':range(1,20+1)+range(230,417+1)},
## {'pdb1':'1ejd','pdb2':'1a2n','chain1':'A','chain2':'A','range':range(20,230+1)},
## ## oligopeptide bp
## {'pdb1':'1rkm','pdb2':'2rkm','chain1':'A','chain2':'A','range':range(1,263+1)+range(491,517+1)},
## {'pdb1':'1rkm','pdb2':'2rkm','chain1':'A','chain2':'A','range':range(277,477+1)},
## ## protein kinase A
## {'pdb1':'1jlu','pdb2':'1cmk','chain1':'E','chain2':'E','range':range(1,33+1)+range(125,310+1),
## {'pdb1':'1jlu','pdb2':'1cmk','chain1':'E','chain2':'E','range':range(34,124+1)},
## ## dna polymerase beta
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(1,82+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(106,132+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(148,262+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(262,335+1)},
## ## ribose bp
## {'pdb1':'1urp','pdb2':'2dri','chain1':'A','chain2':'A','range':range(1,98+1)+range(235,259+1)},
## {'pdb1':'1urp','pdb2':'2dri','chain1':'A','chain2':'A','range':range(104,234+1)+range(265,271+1)},
## ## thioredoxin reductase
## {'pdb1':'1tde','pdb2':'1f6m','chain1':'A','chain2':'E','range':range(1,112+1)+range(248,320+1)},
## {'pdb1':'1tde','pdb2':'1f6m','chain1':'A','chain2':'E','range':range(118,242+1)},
## ## dna bp
## {'pdb1':'1fgu','pdb2':'1jmc','chain1':'A','chain2':'A','range':range(183,283+1)},
## ## transferrin
## {'pdb1':'1bp5','pdb2':'1a8e','chain1':'A','chain2':'A','range':range(1,75+1)+range(249,316+1)},
## {'pdb1':'1bp5','pdb2':'1a8e','chain1':'A','chain2':'A','range':range(103,242+1)},
## ## uracil dna glycosylase
## {'pdb1':'1ssp','pdb2':'1akz','chain1':'E','chain2':'A','range':range(82,144+1)+range(191,240+1)},
## {'pdb1':'1ssp','pdb2':'1akz','chain1':'E','chain2':'A','range':range(166,182+1)+range(270,304+1)},
]
for i in range(len(l_input)):
pdb1 = l_input[i]['pdb1']
pdb2 = l_input[i]['pdb2']
chain1 = l_input[i]['chain1']
chain2 = l_input[i]['chain2']
domain_range = l_input[i]['range']
os.system('cp /oxygenase_local/data/pdb/%s/pdb%s.ent %s.pdb' %(pdb1[1:3],pdb1,pdb1,))
os.system('cp /oxygenase_local/data/pdb/%s/pdb%s.ent %s.pdb' %(pdb2[1:3],pdb2[:4],pdb2[:4],))
ss_range1, l_missing1, seqres1, l_modres = parse_header(pdb1, chain1,)
ss_range2, l_missing2, seqres2, l_modres = parse_header(pdb2[:4], chain2,)
ss_range = list(set(ss_range1)&set(ss_range2))
l_missing = list(set(l_missing1)|set(l_missing2))
if len(seqres1) != len(seqres2):
d_replace = {
'TPO':'THR','PTR':'TYR',
## 'SER':'CYS', ## 1tde v 1f6m
}
for i in range(len(seqres1)):
if seqres1[i] in d_replace.keys():
seqres1[i] = d_replace[seqres1[i]]
for i in range(len(seqres2)):
if seqres2[i] in d_replace.keys():
seqres2[i] = d_replace[seqres2[i]]
if not (''.join(seqres1) in ''.join(seqres2) or ''.join(seqres2) in ''.join(seqres1)):
import sys
sys.path.append('/home/people/tc/svn/EAT_DB/')
import sequence_alignment
d_res = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
seq1 = ''
for res in seqres1:
seq1 += d_res[res]
seq2 = ''
for res in seqres2:
seq2 += d_res[res]
instance = sequence_alignment.NW(seq1,seq2)
s1,s2 = instance.Align(verbose=False)[:2]
l1 = len(s1)-len(s1.lstrip('-'))
l2 = len(s2)-len(s2.lstrip('-'))
r1 = len(s1)-len(s1.rstrip('-'))
r2 = len(s2)-len(s2.rstrip('-'))
print seqres1
print seqres2
print len(seqres1)
print len(seqres2)
print pdb1, pdb2
print l1, l2, r1, r2
print seqres2[l1:len(seqres2)-r1]
print seqres1[l2:len(seqres1)-r2]
l_coordinates1 = parse_coordinates(pdb1,chain1,domain_range,ss_range,l_missing,)
l_coordinates2 = parse_coordinates(pdb2[:4],chain2,domain_range,ss_range,l_missing,)
## l_coordinates1 = l_coordinates1[l2:len(l_coordinates1)-r2]
## l_coordinates2 = l_coordinates2[l1:len(l_coordinates2)-r1]
if len(l_coordinates1) != len(l_coordinates2):
print len(l_coordinates1)
print len(l_coordinates2)
stop
rmsd = instance_geometry.superpose(l_coordinates1,l_coordinates2)
print pdb1, pdb2, round(rmsd,1), len(l_coordinates1)/3.
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
apply_transformation_matrix(
pdb1,chain1,l_modres,
[0,0,0],[[1,0,0],[0,1,0],[0,0,1]],[0,0,0],
)
apply_transformation_matrix(
pdb2,chain2,l_modres,
tv1,rm,tv2,
)
l_coordinates1 = parse_coordinates(pdb1+'_rotated',chain1,range(1,9999),ss_range,l_missing,)
l_coordinates2 = parse_coordinates(pdb2+'_rotated',chain2,range(1,9999),ss_range,l_missing,)
SUM = 0.
n = len(l_coordinates1)
for i in range(n):
SUM += sum((l_coordinates1[i]-l_coordinates2[i])**2)
RMSD = math.sqrt(SUM/n)
print RMSD
return
surfaceloop | volume | physicalsurface | physicalvolume | comment \
| skip1
grammar= OneOrMore(command)+StringEnd()
try:
tokens= grammar.parseFile(filename)
except ParseException, err:
print err.line
print " "*(err.column-1) + "^"
print err
raise err
lineloops={}
surfaceloops={}
g=geom.geometry()
for x in tokens:
if x[0]=="Point":
g.addpoint(int(x[1]),[float(x[2][0]),float(x[2][1]),float(x[2][2])])
elif x[0]=="Line":
assert len(x[2])==2
g.addline(int(x[1]),[int(x[2][0]),int(x[2][1])])
elif x[0]=="Circle":
assert len(x[2])==3
g.addline(int(x[1]),[int(x[2][0]),int(x[2][2])])
#g.add1(geom.circle(int(x[1]),int(x[2][0]),int(x[2][1]),
# int(x[2][2])))
elif x[0]=="Line Loop":
lineloops[int(x[1])]=[int(y) for y in x[2]]
elif x[0]=="Plane Surface":
assert len(x[2])==1
## HEWL scatter plots of RMSD vs misc properties (pH diff, T diff, max resol)
## imports
import os,numpy
import core
import sys
sys.path.append('/home/people/tc/svn/tc_sandbox/pdb')
import parse_mmCIF
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import gnuplot, statistics
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
## appendix
d_321 = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
## exclude/restrict
l_ligands_exclude = [
'IOD', ## 1b2k, 1lkr
'NAG','NDG', ## substrate
'SCN', ## 1lcn, thiocyanate
'CCN', ## acetonitrile cross linker (2lyo,3lyo)
]
def OnClick(self, event):
# inspector = self.parent
wk = self.parent.WorkGroup
ID = event.GetId()
if ID == self.BCK_ID:
self.parent.ShowAction(self.parent.geometryActions)
if ID == self.EMP_ID:
geo = cad_geometry()
wk.add_geometry(geometry(geo))
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = cad_geometry()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.LIN_ID:
from caid.cad_geometry import line as domain
geo = domain()
wk.add_geometry(geometry(geo))
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = line()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.LNR_ID:
self.parent.objectActionsCreateLinear.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateLinear)
if ID == self.ARC_ID:
self.parent.objectActionsCreateArc.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateArc)
if ID == self.CRV_ID:
self.parent.objectActionsCurve.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCurve)
if ID == self.SQR_ID:
from caid.cad_geometry import square as domain
geo = domain()
wk.add_geometry(geometry(geo))
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = square()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.BIL_ID:
self.parent.objectActionsCreateBilinear.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateBilinear)
if ID == self.CRC_ID:
self.parent.objectActionsCreateCircle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateCircle)
if ID == self.QCR_ID:
self.parent.objectActionsCreateQuartCircle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateQuartCircle)
if ID == self.ANL_ID:
self.parent.objectActionsCreateAnnulus.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateAnnulus)
if ID == self.CR5_ID:
self.parent.objectActionsCreateCircle_5mp.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateCircle_5mp)
if ID == self.TRL_ID:
self.parent.objectActionsCreateTriangle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateTriangle)
def OnClick(self, event):
ID = event.GetId()
if ID == self.BCK_ID:
self.parent.ShowAction(self.parent.geometryActions)
if ID == self.GO_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
_geo = cad_geometry()
for nrb in geo:
geo_t = cad_geometry()
geo_t.append(nrb)
# ... refinement
list_t = None
if self.n.sum() > 0:
list_t = []
for axis in range(0,nrb.dim):
ub = nrb.knots[axis][0]
ue = nrb.knots[axis][-1]
t = []
if self.n[axis] > 0:
t = np.linspace(ub,ue,self.n[axis]+2)[1:-1]
list_t.append(t)
list_p = None
if self.p.sum() > 0:
list_p = []
for axis in range(0,nrb.dim):
list_p.append(np.max(self.p[axis] - nrb.degree[axis], 0))
list_m = None
if self.m.sum() > 0:
list_m = []
for axis in range(0,nrb.dim):
list_m.append(self.m[axis])
geo_t.refine(list_t=list_t, list_p=list_p, list_m=list_m)
_geo.append(geo_t[0])
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... refine geometry")
macro_script.append("_geo = cad_geometry()")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("for nrb in geo:")
macro_script.append("\tgeo_t = cad_geometry()")
macro_script.append("\tgeo_t.append(nrb)")
str_list_t = [list(ts) for ts in list_t]
macro_script.append("\tlist_t = "+ str(str_list_t))
macro_script.append("\tlist_p = "+ str(list_p))
macro_script.append("\tlist_m = "+ str(list_m))
macro_script.append("\tgeo_t.refine(list_t=list_t, list_p=list_p, list_m=list_m)")
macro_script.append("\t_geo.append(geo_t[0])")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
# ...
_geo.set_internal_faces(geo.internal_faces)
_geo.set_external_faces(geo.external_faces)
_geo.set_connectivity(geo.connectivity)
geo_new = geometry(_geo)
geo_newItem = wk.add_geometry(geo_new)
def main(self, pdb1, pdb2, chains1, chains2):
import Numeric, math, os
import quakes
instance_quakes = quakes.quakes()
import sys
sys.path.append('/home/people/tc/python/Protool/')
import geometry
instance_geometry = geometry.geometry()
pdbs = [pdb1,pdb2]
##
## parse coordinates to dictionary
##
d_noncoordinates = {}
d_coordinates = {}
for pdb in pdbs:
## read pdb file
fd = open('%s%s.pdb' %(self.pdbpath, pdb),'r')
lines = fd.readlines()
fd.close()
## parse pdb file
d_noncoords = instance_quakes.parse_pdbnoncoordinatesections(lines, pdb)
d_coords = instance_quakes.parse_pdbcoordinatesection(lines, pdb)
d_noncoordinates[pdb] = d_noncoords
d_coordinates[pdb] = d_coords
##
## convert dictionary of coordinates to list of coordinates
##
coordinates1 = []
coordinates2 = []
d_alignATOMseq = {}
for i in range(len(chains1)):
chain1 = chains1[i]
chain2 = chains2[i]
d_res_nos1, d_res_nos2, l1, l2, ATOMseq1, ATOMseq2 = instance_quakes.alignATOMseq(d_coordinates, d_noncoordinates, pdb1, pdb2, chain1, chain2)
d_alignATOMseq[chain2] = {}
d_alignATOMseq[chain2]['d_res_nos1'] = d_res_nos1
d_alignATOMseq[chain2]['d_res_nos2'] = d_res_nos2
d_alignATOMseq[chain2]['l1'] = l1
d_alignATOMseq[chain2]['l2'] = l2
coords1, coords2, rescount = instance_quakes.ATOMrecords2coordinates(d_coordinates, pdb1, pdb2, chain1, chain2, d_res_nos1, d_res_nos2, l1, l2, ATOMseq1, ATOMseq2)
coordinates1 += coords1
coordinates2 += coords2
##
## align coordinates
##
rmsd = instance_geometry.superpose(coordinates1,coordinates2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
##
## calculate RMSD of transformed coordinates of individual residues
##
lines1 = []
lines2 = []
atom_no = 0
for i in range(len(chains1)):
chain1 = chains1[i]
chain2 = chains2[i]
for SEQRESpos1 in range(l2,len(ATOMseq1)+l2):
SEQRESpos2 = SEQRESpos1+l1-l2
res_no1 = d_res_nos1[SEQRESpos1]['res_no']
res_no2 = d_res_nos2[SEQRESpos2]['res_no']
if res_no1 == '-' or res_no2 == '-':
continue
iCode1 = d_res_nos1[SEQRESpos1]['iCode']
iCode2 = d_res_nos2[SEQRESpos2]['iCode']
if res_no1 not in d_coordinates[pdb1]['chains'][chain1]['residues'].keys():
continue
if res_no2 not in d_coordinates[pdb2]['chains'][chain2]['residues'].keys():
continue
if 'REMARK' in d_coordinates[pdb1]['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1].keys():
continue
if 'REMARK' in d_coordinates[pdb2]['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2].keys():
continue
d_resname = {
pdb1:{'chain':chain1,'res_no':res_no1,'iCode':iCode1},
pdb2:{'chain':chain2,'res_no':res_no2,'iCode':iCode2},
}
for pdb in d_resname.keys():
chain = d_resname[pdb]['chain']
res_no = d_resname[pdb]['res_no']
iCode = d_resname[pdb]['iCode']
res_name = d_coordinates[pdb]['chains'][chain]['residues'][res_no]['d_iCodes'][iCode]['res_name']
d_atoms = d_coordinates[pdb]['chains'][chain]['residues'][res_no]['d_iCodes'][iCode]['atoms']
d_resname[pdb]['res_name'] = res_name
d_resname[pdb]['d_atoms'] = d_atoms
res_name1 = d_resname[pdb1]['res_name']
res_name2 = d_resname[pdb2]['res_name']
d_atoms1 = d_resname[pdb1]['d_atoms']
d_atoms2 = d_resname[pdb2]['d_atoms']
## print pdb1, pdb2, chain1, chain2, res_no1, res_no2, res_name1, res_name2
##
## calculate rmsd for the atoms of the residue
##
SS = []
for atom_name in d_atoms1.keys():
if atom_name not in d_atoms2.keys():
continue
coordinate1 = d_atoms1[atom_name]['coordinate']
coordinate2 = Numeric.matrixmultiply(rm, d_atoms2[atom_name]['coordinate']-tv1)+tv2
SS += [sum((coordinate2-coordinate1)**2)]
RMSD = math.sqrt(sum(SS)/len(SS))
occupancy = bfactor = RMSD/rmsd
##
## append atoms and coordinates to lines
##
for atom_name in d_atoms1.keys():
if atom_name not in d_atoms2.keys():
continue
coordinate1 = d_atoms1[atom_name]['coordinate']
coordinate2 = d_atoms2[atom_name]['coordinate']
x1 = coordinate1[0]; y1 = coordinate1[1]; z1 = coordinate1[2]
x2 = coordinate2[0]; y2 = coordinate2[1]; z2 = coordinate1[2]
atom_no += 1
altloc = ''
charge = ''
if 'H' in atom_name:
element = 'H'
else:
element = atom_name[0]
lines1 += [
'%6s%5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s\n'
%('ATOM'.ljust(6), atom_no, atom_name.ljust(4), altloc, res_name1.ljust(3), chain1, res_no1, iCode1, x1, y1, z1, occupancy, bfactor, element.rjust(2), charge.rjust(2))
]
lines2 += [
'%6s%5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s\n'
%('ATOM'.ljust(6), atom_no, atom_name.ljust(4), altloc, res_name2.ljust(3), chain2, res_no2, iCode2, x2, y2, z2, occupancy, bfactor, element.rjust(2), charge.rjust(2))
]
fd = open('%s%s.pdb' %(self.path_out,pdb1),'w')
fd.writelines(lines1)
fd.close()
fd = open('%s%s.pdb' %(self.path_out,pdb2),'w')
fd.writelines(lines2)
fd.close()
for pdb in pdbs:
## write rasmol script
lines = [
'rasmol -nodisplay %s%s.pdb << EOF\n' %(self.path_out,pdb),
'color temperature\n',
'spacefill\n',
'write %s%s.ppm\n' %(self.path_tmp,pdb),
'exit\n',
]
## write rasmol script to file
fd = open('%s%srasmol.src' %(self.path_tmp,pdb),'w')
fd.writelines(lines)
fd.close()
## execute rasmol script
os.system('source %s%srasmol.src' %(self.path_tmp,pdb))
## convert rasmol output
os.system('convert %s%s.ppm -resize x80 %s%s.gif' %(self.path_tmp,pdb, self.path_out,pdb))
## clean up
os.system('rm %s%s.ppm' %(self.path_tmp,pdb))
## clean up
os.system('rm %s%srasmol.src' %(self.path_tmp,pdb))
os.system
return
class MyApp(wx.App):
"""Our application class
"""
def OnInit(self):
"""Initialize by creating the split window with the tree
"""
frame = Inspector(None, -1, "Inspector")
frame.Show(True)
self.SetTopWindow(frame)
self.frame = frame
return True
if __name__ == "__main__":
app = MyApp(0)
frame = app.frame
tree = frame.tree
from caid.cad_geometry import circle_5mp, square
s1 = circle_5mp()
s2 = square()
geo1 = geometry(s1)
geo2 = geometry(s2)
tree.add_geometry(geo1)
tree.add_geometry(geo2)
app.MainLoop()
def main(pdb1,pdb2,chains1_align,chains2_align,):
chains1_apply = chains1_align
chains2_apply = chains2_align
import os, sys, math
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
domain_range = range(0,9999)
os.system('cp /data/pdb-v3.2/%s/pdb%s.ent %s.pdb' %(pdb1[1:3],pdb1,pdb1,))
os.system('cp /data/pdb-v3.2/%s/pdb%s.ent %s.pdb' %(pdb2[1:3],pdb2,pdb2,))
ss_range1, l_missing1, seqres1, l_modres = parse_header(pdb1, chains1_align,)
ss_range2, l_missing2, seqres2, l_modres = parse_header(pdb2, chains2_align,)
ss_range = list(set(ss_range1)&set(ss_range2))
l_missing = list(set(l_missing1)|set(l_missing2))
if len(seqres1) != len(seqres2):
d_replace = {
'TPO':'THR','PTR':'TYR',
## 'SER':'CYS', ## 1tde v 1f6m
}
for i in range(len(seqres1)):
if seqres1[i] in d_replace.keys():
seqres1[i] = d_replace[seqres1[i]]
for i in range(len(seqres2)):
if seqres2[i] in d_replace.keys():
seqres2[i] = d_replace[seqres2[i]]
if not (''.join(seqres1) in ''.join(seqres2) or ''.join(seqres2) in ''.join(seqres1)):
import sys
sys.path.append('/home/people/tc/svn/EAT_DB/')
import sequence_alignment
d_res = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
seq1 = ''
for res in seqres1:
seq1 += d_res[res]
seq2 = ''
for res in seqres2:
seq2 += d_res[res]
instance = sequence_alignment.NW(seq1,seq2)
s1,s2 = instance.Align(verbose=False)[:2]
l1 = len(s1)-len(s1.lstrip('-'))
l2 = len(s2)-len(s2.lstrip('-'))
r1 = len(s1)-len(s1.rstrip('-'))
r2 = len(s2)-len(s2.rstrip('-'))
print seqres1
print seqres2
print len(seqres1)
print len(seqres2)
print pdb1, pdb2
print l1, l2, r1, r2
print seqres2[l1:len(seqres2)-r1]
print seqres1[l2:len(seqres1)-r2]
else:
s1 = ''.join(seqres1)
s2 = ''.join(seqres2)
if s1 in s2:
seqres2 = seqres2[s2.index(s1)/3:]
else:
seqres1 = seqres1[s1.index(s2)/3:]
if len(seqres1) != len(seqres2):
print len(seqres1), len(seqres2)
stop
l_coordinates1 = parse_coordinates(pdb1,chains1_align,domain_range,ss_range,l_missing,)
l_coordinates2 = parse_coordinates(pdb2,chains2_align,domain_range,ss_range,l_missing,)
## l_coordinates1 = l_coordinates1[l2:len(l_coordinates1)-r2]
## l_coordinates2 = l_coordinates2[l1:len(l_coordinates2)-r1]
if len(l_coordinates1) == 0 or len(l_coordinates2) == 0:
stop
if len(l_coordinates1) != len(l_coordinates2):
print len(l_coordinates1)
print len(l_coordinates2)
stop
rmsd = instance_geometry.superpose(l_coordinates1,l_coordinates2)
print pdb1, pdb2
print 'rmsd', round(rmsd,1)
print 'residues', len(seqres1), len(seqres2)
print 'coordinates', len(l_coordinates1)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
lines1 = apply_transformation_matrix(
pdb1,chains1_apply,l_modres,
[0,0,0],[[1,0,0],[0,1,0],[0,0,1]],[0,0,0],
)
lines2 = apply_transformation_matrix(
pdb2,chains2_apply,l_modres,
tv1,rm,tv2,
)
fd = open('rotated_%s%s.pdb' %(pdb1,pdb2,),'w')
fd.writelines(lines1+lines2)
fd.close()
l_coordinates1 = parse_coordinates('rotated_'+pdb1,chains1_apply,range(-9999,9999),ss_range,l_missing,)
l_coordinates2 = parse_coordinates('rotated_'+pdb2,chains2_apply,range(-9999,9999),ss_range,l_missing,)
SUM = 0.
n = len(l_coordinates1)
for i in range(n):
SUM += sum((l_coordinates1[i]-l_coordinates2[i])**2)
RMSD = math.sqrt(SUM/n)
print 'RMSD all atoms', RMSD
return RMSD,l_coordinates1,l_coordinates2
wk = self.WorkGroup
keycode = event.GetKeyCode()
if keycode == wx.WXK_DELETE:
wk.directAct.removeObject()
class MyApp(wx.App):
'''Our application class
'''
def OnInit(self):
'''Initialize by creating the split window with the tree
'''
frame = Inspector(None, -1, 'Inspector')
frame.Show(True)
self.SetTopWindow(frame)
self.frame = frame
return True
if __name__ == '__main__':
app = MyApp(0)
frame = app.frame
tree = frame.tree
from caid.cad_geometry import circle_5mp, square
s1 = circle_5mp()
s2 = square()
geo1 = geometry(s1)
geo2 = geometry(s2)
tree.add_geometry(geo1)
tree.add_geometry(geo2)
app.MainLoop()
def OnClick(self, event):
ID = event.GetId()
if ID == self.NEW_ID:
self.parent.ShowAction(self.parent.geometryActionsNew)
if ID == self.ADD_ID:
self.parent.ShowAction(self.parent.geometryActionsAdd)
if ID == self.DEL_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo_id = wk.list_geo.index(geo)
wk.remove_geometry(geoItem, geo)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... delete geometry")
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geoItem = geo.treeItem")
macro_script.append("wk.remove_geometry(geoItem, geo)")
macro_script.append("# ...")
if ID == self.DUP_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo_new = wk.inspector.currentGeometry.copy()
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... copy geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("_geo = geo.copy()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.PLJ_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
import matplotlib.pyplot as plt
try:
MeshResolution = geo.list_patchInfo[0].steps[0]
except:
MeshResolution = 10
geo.plotJacobians(MeshResolution=MeshResolution)
plt.colorbar()
plt.show()
if ID == self.PLM_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
import matplotlib.pyplot as plt
MeshResolution = geo.list_patchInfo[0].steps[0]
geo.plotMesh(MeshResolution=MeshResolution)
plt.show()
if ID == self.EXP_ID:
from global_vars import CAIDwildcard
# Create a save file dialog
dialog = wx.FileDialog ( None, style = wx.SAVE | wx.OVERWRITE_PROMPT
, wildcard=CAIDwildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
ls_file = dialog.GetPath()
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geo.save(ls_file)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... export geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("filename = \""+ls_file+"\"")
macro_script.append("geo.save(filename)")
macro_script.append("# ...")
# Destroy the dialog
dialog.Destroy()
if ID == self.EDT_ID:
from Editor import Editor
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
edt = Editor(wk.parent, -1, 'Editor')
filename = edt.DoOpenGeometryAsFile(geo)
# wait until the editor is closed
createNewGeo = False
while edt:
if edt.modify:
createNewGeo = True
wx.MilliSleep(10)
wx.GetApp().Yield()
if createNewGeo:
newgeo = cad_geometry(filename)
geo_new = geometry(newgeo)
geo_newItem = wk.add_geometry(geo_new)
try:
os.remove(filename)
except:
pass
if ID == self.TRS_ID:
self.parent.objectActionsTranslate.asGeometry()
self.parent.ShowAction(self.parent.objectActionsTranslate)
if ID == self.ROT_ID:
self.parent.objectActionsRotate.asGeometry()
self.parent.ShowAction(self.parent.objectActionsRotate)
if ID == self.SCL_ID:
self.parent.objectActionsScale.asGeometry()
self.parent.ShowAction(self.parent.objectActionsScale)
if ID == self.REF_ID:
self.parent.ShowAction(self.parent.geometryActionsRefine)
if ID == self.PEX_ID:
self.parent.objectActionsPolarExtrude.asGeometry()
self.parent.ShowAction(self.parent.objectActionsPolarExtrude)
if ID == self.EXD_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
list_geo = geo.expand()
for _geo in list_geo:
geo_new = geometry(_geo)
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... expand geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("list_geo = geo.expand()")
macro_script.append("for _geo in list_geo:")
macro_script.append("\twk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.IMP_ID:
# Create an open file dialog
dialog = wx.FileDialog(None, style = wx.OPEN)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
filename = dialog.GetPath()
# TODO update recent files
# self.UpdateRecentFiles(filename)
geo = cad_geometry(filename)
wk = self.parent.WorkGroup
wk.add_geometry(geometry(geo))
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... import geometry")
macro_script.append("filename = \""+filename+"\"")
macro_script.append("_geo = cad_geometry(filename)")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
# Destroy the dialog
dialog.Destroy()
if ID == self.REI_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo.initialize_info()
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... initialize info geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geo.initialize_info()")
macro_script.append("wk.Refresh(inspector=True)")
macro_script.append("# ...")
wk.Refresh(inspector=True)
if ID == self.UPI_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo.update()
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... update geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geo.update()")
macro_script.append("wk.Refresh(inspector=True)")
macro_script.append("# ...")
wk.Refresh(inspector=True)
if ID == self.T5P_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
item = wk.inspector.tree.GetSelection()
geo_bnd = wk.inspector.tree.GetPyData(item)
face = geo_bnd.face
faceItem = wk.inspector.tree.GetItemParent(item)
patchItem = wk.inspector.tree.GetItemParent(faceItem)
geoItem = wk.inspector.tree.GetItemParent(patchItem)
geo = wk.inspector.tree.GetPyData(geoItem)
_geo = cad_geometry()
_geo.append(geo[0])
geo_new = geometry(_geo.to5patchs(face))
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... to-5-patchs geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = "+str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("_geo = cad_geometry()")
macro_script.append("_geo.append(geo[0])")
macro_script.append("face = "+str(face))
macro_script.append("_geo = _geo.to5patchs(face)")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("wk.Refresh()")
macro_script.append("# ...")
wk.Refresh()
def OnClick(self, event):
# inspector = self.parent
wk = self.parent.WorkGroup
ID = event.GetId()
if ID == self.BCK_ID:
self.parent.ShowAction(self.parent.geometryActions)
if ID == self.EMP_ID:
geo = cad_geometry()
wk.add_geometry(geometry(geo))
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = cad_geometry()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.LIN_ID:
from caid.cad_geometry import line as domain
geo = domain()
wk.add_geometry(geometry(geo))
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = line()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.LNR_ID:
self.parent.objectActionsCreateLinear.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateLinear)
if ID == self.ARC_ID:
self.parent.objectActionsCreateArc.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateArc)
if ID == self.CRV_ID:
self.parent.objectActionsCurve.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCurve)
if ID == self.SQR_ID:
from caid.cad_geometry import square as domain
geo = domain()
wk.add_geometry(geometry(geo))
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... create object")
macro_script.append("_geo = square()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.BIL_ID:
self.parent.objectActionsCreateBilinear.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateBilinear)
if ID == self.CRC_ID:
self.parent.objectActionsCreateCircle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateCircle)
if ID == self.QCR_ID:
self.parent.objectActionsCreateQuartCircle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateQuartCircle)
if ID == self.ANL_ID:
self.parent.objectActionsCreateAnnulus.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateAnnulus)
if ID == self.CR5_ID:
self.parent.objectActionsCreateCircle_5mp.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateCircle_5mp)
if ID == self.PC5_ID:
self.parent.objectActionsCreatePinched_Circle_5mp.asGeometry()
self.parent.ShowAction(
self.parent.objectActionsCreatePinched_Circle_5mp)
if ID == self.TRL_ID:
self.parent.objectActionsCreateTriangle.asGeometry()
self.parent.ShowAction(self.parent.objectActionsCreateTriangle)
if ID == self.CUB_ID:
# from caid.cad_geometry import cube as domain
from caid.cad_geometry import trilinear as domain
geo = domain()
wk.add_geometry(geometry(geo))
def main():
import os, sys, math
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
## ## lactoferrin
## pdb1 = '1lfg'
## pdb2 = '1lfh'
## domain_range = range(1,88+1)+range(253,333+1)
## chain = 'A'
## ## trp repressor
## pdb1 = '1wrp'
## pdb2 = '2oz9' ## 2wrp
## pdb2 = '1zt9'
## domain_range = range(1,999+1)
## chain1 = 'R'
## chain2 = 'R'
## chain2 = 'A'
## exclude_chain = ''
## ## luciferase
## pdb1 = '1ba3'
## pdb2 = '1lci'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = ''
## ## G3P DH
## pdb1 = '1gd1'
## pdb2 = '2gd1'
## domain_range = range(1,999+1)
## chain1 = 'O'
## chain2 = 'O'
## exclude_chain = ''
## ## hexokinase
## pdb1 = '1hkg'
## pdb2 = '2yhx'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = ''
## ## adk
## pdb1 = '1ake'
## pdb2 = '4ake'
## domain_range = range(1,999+1)
## chain1 = 'A'
## chain2 = 'A'
## exclude_chain = 'B'
## ## t4l
## pdb1 = '2lzm'
## pdb2 = '150l'
#### domain_range = range(15,59+1)
#### domain_range = range(60,80+1)
## domain_range = range(81,162+1)
## chain1 = 'A'
## chain2 = 'D'
## exclude_chain = 'B'
l_input = [
## ##
## {'pdb1':'1ipd','pdb2':'1osj','chain1':'A','chain2':'A','range':range(1,98+1)+range(253,345+1)},
## {'pdb1':'1ipd','pdb2':'1osj','chain1':'A','chain2':'A','range':range(99,108+1)+range(109,252+1)},
###### shears
## ## aspartate amino transferase
## {'pdb1':'9aat','pdb2':'1ama','chain1':'A','chain2':'A','range':range(15,36+1)+range(349,410+1)},
## {'pdb1':'9aat','pdb2':'1ama','chain1':'A','chain2':'A','range':range(50,312+1)},
## alcohol dehydrogenase
{
'pdb1': '6adh',
'pdb2': '8adh1',
'chain1': 'A',
'chain2': 'A',
'range': range(1, 174 + 1) + range(322, 374 + 1)
},
{
'pdb1': '6adh',
'pdb2': '8adh2',
'chain1': 'A',
'chain2': 'A',
'range': range(193, 317 + 1)
},
## ## citrate synthase
## {'pdb1':'1cts','pdb2':'4cts','chain1':'A','chain2':'A','range':range(1,276+1)+range(386,999+1)},
###### hinges
## ## atpsulf
## {'pdb1':'1i2d','pdb2':'1m8p','chain1':'A','chain2':'A','range':range(1,389+1)},
## ## dnak (different spacegroups)
## {'pdb1':'1dkx','pdb2':'1dky','chain1':'A','chain2':'A','range':range(389,509+1)},
## ## dnak (different spacegroups)
## {'pdb1':'1ddt','pdb2':'1mdt','chain1':'A','chain2':'A','range':range(1,376+1)},
## ## ecpdpbp
## {'pdb1':'1dpp','pdb2':'1dpe','chain1':'A','chain2':'A','range':range(1,260+1)+range(479,999+1)},
## ## ef2
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(1,478+1)}, ## large
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(479,560+1)}, ## independent
## {'pdb1':'1n0v','pdb2':'1n0u','chain1':'C','chain2':'A','range':range(561,9999+1)}, ## small
## ## febp
## {'pdb1':'1d9v','pdb2':'1mrp','chain1':'A','chain2':'A','range':range(109,227+1)+range(292,309+1)},
## {'pdb1':'1d9v','pdb2':'1mrp','chain1':'A','chain2':'A','range':range(1,96+1)+range(228,262+1)},
## ## folylpolyglutamate synthetase
## {'pdb1':'1jbv','pdb2':'1jbw','chain1':'A','chain2':'A','range':range(1,295+1)},
## {'pdb1':'1jbv','pdb2':'1jbw','chain1':'A','chain2':'A','range':range(296,386+1)},
## ## glucose ABC transporter ATPase subunit (different spacegroups)
## {'pdb1':'1oxs','pdb2':'1oxu','chain1':'C','chain2':'C','range':range(1,209+1)},
## {'pdb1':'1oxs','pdb2':'1oxu','chain1':'C','chain2':'C','range':range(244,999+1)},
## ## groel domain
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(1,137+1)+range(410,999+1)},
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(192,374+1)},
## {'pdb1':'1aon','pdb2':'1oel','chain1':'A','chain2':'A','range':range(138,190+1)+range(375,409+1)},
## ## lao bp
## {'pdb1':'2lao','pdb2':'1laf','chain1':'A','chain2':'E','range':range(1,90+1)+range(192,238+1)},
## {'pdb1':'2lao','pdb2':'1laf','chain1':'A','chain2':'E','range':range(91,191+1)},
## ## t4l
## {'pdb1':'1l96','pdb2':'1l97','chain1':'A','chain2':'A','range':range(13,59+1)},
## {'pdb1':'1l96','pdb2':'1l97','chain1':'A','chain2':'A','range':range(81,164+1)},
## ## maltodextrin bp
## {'pdb1':'1omp','pdb2':'3mbp','chain1':'A','chain2':'A','range':range(1,104+1)+range(268,313+1)},
## {'pdb1':'1omp','pdb2':'3mbp','chain1':'A','chain2':'A','range':range(113,258+1)+range(314,370+1)},
## ## mRNA capping enzyme
## {'pdb1':'1ckm','pdb2':'1ckm','chain1':'A','chain2':'B','range':range(1,237+1)+range(319,327+1)},
## {'pdb1':'1ckm','pdb2':'1ckm','chain1':'A','chain2':'B','range':range(241,303+1)},
## ## mura
## {'pdb1':'1ejd','pdb2':'1a2n','chain1':'A','chain2':'A','range':range(1,20+1)+range(230,417+1)},
## {'pdb1':'1ejd','pdb2':'1a2n','chain1':'A','chain2':'A','range':range(20,230+1)},
## ## oligopeptide bp
## {'pdb1':'1rkm','pdb2':'2rkm','chain1':'A','chain2':'A','range':range(1,263+1)+range(491,517+1)},
## {'pdb1':'1rkm','pdb2':'2rkm','chain1':'A','chain2':'A','range':range(277,477+1)},
## ## protein kinase A
## {'pdb1':'1jlu','pdb2':'1cmk','chain1':'E','chain2':'E','range':range(1,33+1)+range(125,310+1),
## {'pdb1':'1jlu','pdb2':'1cmk','chain1':'E','chain2':'E','range':range(34,124+1)},
## ## dna polymerase beta
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(1,82+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(106,132+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(148,262+1)},
## {'pdb1':'1bpd','pdb2':'2bpg','chain1':'A','chain2':'A','range':range(262,335+1)},
## ## ribose bp
## {'pdb1':'1urp','pdb2':'2dri','chain1':'A','chain2':'A','range':range(1,98+1)+range(235,259+1)},
## {'pdb1':'1urp','pdb2':'2dri','chain1':'A','chain2':'A','range':range(104,234+1)+range(265,271+1)},
## ## thioredoxin reductase
## {'pdb1':'1tde','pdb2':'1f6m','chain1':'A','chain2':'E','range':range(1,112+1)+range(248,320+1)},
## {'pdb1':'1tde','pdb2':'1f6m','chain1':'A','chain2':'E','range':range(118,242+1)},
## ## dna bp
## {'pdb1':'1fgu','pdb2':'1jmc','chain1':'A','chain2':'A','range':range(183,283+1)},
## ## transferrin
## {'pdb1':'1bp5','pdb2':'1a8e','chain1':'A','chain2':'A','range':range(1,75+1)+range(249,316+1)},
## {'pdb1':'1bp5','pdb2':'1a8e','chain1':'A','chain2':'A','range':range(103,242+1)},
## ## uracil dna glycosylase
## {'pdb1':'1ssp','pdb2':'1akz','chain1':'E','chain2':'A','range':range(82,144+1)+range(191,240+1)},
## {'pdb1':'1ssp','pdb2':'1akz','chain1':'E','chain2':'A','range':range(166,182+1)+range(270,304+1)},
]
for i in range(len(l_input)):
pdb1 = l_input[i]['pdb1']
pdb2 = l_input[i]['pdb2']
chain1 = l_input[i]['chain1']
chain2 = l_input[i]['chain2']
domain_range = l_input[i]['range']
os.system('cp /oxygenase_local/data/pdb/%s/pdb%s.ent %s.pdb' % (
pdb1[1:3],
pdb1,
pdb1,
))
os.system('cp /oxygenase_local/data/pdb/%s/pdb%s.ent %s.pdb' % (
pdb2[1:3],
pdb2[:4],
pdb2[:4],
))
ss_range1, l_missing1, seqres1, l_modres = parse_header(
pdb1,
chain1,
)
ss_range2, l_missing2, seqres2, l_modres = parse_header(
pdb2[:4],
chain2,
)
ss_range = list(set(ss_range1) & set(ss_range2))
l_missing = list(set(l_missing1) | set(l_missing2))
if len(seqres1) != len(seqres2):
d_replace = {
'TPO': 'THR',
'PTR': 'TYR',
## 'SER':'CYS', ## 1tde v 1f6m
}
for i in range(len(seqres1)):
if seqres1[i] in d_replace.keys():
seqres1[i] = d_replace[seqres1[i]]
for i in range(len(seqres2)):
if seqres2[i] in d_replace.keys():
seqres2[i] = d_replace[seqres2[i]]
if not (''.join(seqres1) in ''.join(seqres2)
or ''.join(seqres2) in ''.join(seqres1)):
import sys
sys.path.append('/home/people/tc/svn/EAT_DB/')
import sequence_alignment
d_res = {
'ALA': 'A',
'CYS': 'C',
'ASP': 'D',
'GLU': 'E',
'PHE': 'F',
'GLY': 'G',
'HIS': 'H',
'ILE': 'I',
'LYS': 'K',
'LEU': 'L',
'MET': 'M',
'ASN': 'N',
'PRO': 'P',
'GLN': 'Q',
'ARG': 'R',
'SER': 'S',
'THR': 'T',
'VAL': 'V',
'TRP': 'W',
'TYR': 'Y',
}
seq1 = ''
for res in seqres1:
seq1 += d_res[res]
seq2 = ''
for res in seqres2:
seq2 += d_res[res]
instance = sequence_alignment.NW(seq1, seq2)
s1, s2 = instance.Align(verbose=False)[:2]
l1 = len(s1) - len(s1.lstrip('-'))
l2 = len(s2) - len(s2.lstrip('-'))
r1 = len(s1) - len(s1.rstrip('-'))
r2 = len(s2) - len(s2.rstrip('-'))
print seqres1
print seqres2
print len(seqres1)
print len(seqres2)
print pdb1, pdb2
print l1, l2, r1, r2
print seqres2[l1:len(seqres2) - r1]
print seqres1[l2:len(seqres1) - r2]
l_coordinates1 = parse_coordinates(
pdb1,
chain1,
domain_range,
ss_range,
l_missing,
)
l_coordinates2 = parse_coordinates(
pdb2[:4],
chain2,
domain_range,
ss_range,
l_missing,
)
## l_coordinates1 = l_coordinates1[l2:len(l_coordinates1)-r2]
## l_coordinates2 = l_coordinates2[l1:len(l_coordinates2)-r1]
if len(l_coordinates1) != len(l_coordinates2):
print len(l_coordinates1)
print len(l_coordinates2)
stop
rmsd = instance_geometry.superpose(l_coordinates1, l_coordinates2)
print pdb1, pdb2, round(rmsd, 1), len(l_coordinates1) / 3.
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
apply_transformation_matrix(
pdb1,
chain1,
l_modres,
[0, 0, 0],
[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
[0, 0, 0],
)
apply_transformation_matrix(
pdb2,
chain2,
l_modres,
tv1,
rm,
tv2,
)
l_coordinates1 = parse_coordinates(
pdb1 + '_rotated',
chain1,
range(1, 9999),
ss_range,
l_missing,
)
l_coordinates2 = parse_coordinates(
pdb2 + '_rotated',
chain2,
range(1, 9999),
ss_range,
l_missing,
)
SUM = 0.
n = len(l_coordinates1)
for i in range(n):
SUM += sum((l_coordinates1[i] - l_coordinates2[i])**2)
RMSD = math.sqrt(SUM / n)
print RMSD
return
def OnClick(self, event):
ID = event.GetId()
if ID == self.NEW_ID:
self.parent.ShowAction(self.parent.geometryActionsNew)
if ID == self.ADD_ID:
self.parent.ShowAction(self.parent.geometryActionsAdd)
if ID == self.DEL_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo_id = wk.list_geo.index(geo)
wk.remove_geometry(geoItem, geo)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... delete geometry")
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geoItem = geo.treeItem")
macro_script.append("wk.remove_geometry(geoItem, geo)")
macro_script.append("# ...")
if ID == self.DUP_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geo_new = wk.inspector.currentGeometry.copy()
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... copy geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("_geo = geo.copy()")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.PLJ_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
import matplotlib.pyplot as plt
try:
MeshResolution = geo.list_patchInfo[0].steps[0]
except:
MeshResolution = 10
geo.plotJacobians(MeshResolution=MeshResolution)
plt.colorbar()
plt.show()
if ID == self.PLM_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
import matplotlib.pyplot as plt
MeshResolution = geo.list_patchInfo[0].steps[0]
geo.plotMesh(MeshResolution=MeshResolution)
plt.show()
if ID == self.EXP_ID:
from global_vars import CAIDwildcard
# Create a save file dialog
dialog = wx.FileDialog(None,
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT,
wildcard=CAIDwildcard)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
ls_file = dialog.GetPath()
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geo.save(ls_file)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... export geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("filename = \"" + ls_file + "\"")
macro_script.append("geo.save(filename)")
macro_script.append("# ...")
# Destroy the dialog
dialog.Destroy()
if ID == self.EDT_ID:
from Editor import Editor
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
edt = Editor(wk.parent, -1, 'Editor')
filename = edt.DoOpenGeometryAsFile(geo)
# wait until the editor is closed
createNewGeo = False
while edt:
if edt.modify:
createNewGeo = True
wx.MilliSleep(10)
wx.GetApp().Yield()
if createNewGeo:
newgeo = cad_geometry(filename)
geo_new = geometry(newgeo)
geo_newItem = wk.add_geometry(geo_new)
try:
os.remove(filename)
except:
pass
if ID == self.TRS_ID:
self.parent.objectActionsTranslate.asGeometry()
self.parent.ShowAction(self.parent.objectActionsTranslate)
if ID == self.ROT_ID:
self.parent.objectActionsRotate.asGeometry()
self.parent.ShowAction(self.parent.objectActionsRotate)
if ID == self.SCL_ID:
self.parent.objectActionsScale.asGeometry()
self.parent.ShowAction(self.parent.objectActionsScale)
if ID == self.REF_ID:
self.parent.ShowAction(self.parent.geometryActionsRefine)
if ID == self.PEX_ID:
self.parent.objectActionsPolarExtrude.asGeometry()
self.parent.ShowAction(self.parent.objectActionsPolarExtrude)
if ID == self.EXD_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
list_geo = geo.expand()
for _geo in list_geo:
geo_new = geometry(_geo)
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... expand geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("list_geo = geo.expand()")
macro_script.append("for _geo in list_geo:")
macro_script.append("\twk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
if ID == self.IMP_ID:
# Create an open file dialog
dialog = wx.FileDialog(None, style=wx.FD_OPEN)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
filename = dialog.GetPath()
# TODO update recent files
# self.UpdateRecentFiles(filename)
geo = cad_geometry(filename)
wk = self.parent.WorkGroup
wk.add_geometry(geometry(geo))
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... import geometry")
macro_script.append("filename = \"" + filename + "\"")
macro_script.append("_geo = cad_geometry(filename)")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("# ...")
# Destroy the dialog
dialog.Destroy()
if ID == self.REI_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo.initialize_info()
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... initialize info geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geo.initialize_info()")
macro_script.append("wk.Refresh(inspector=True)")
macro_script.append("# ...")
wk.Refresh(inspector=True)
if ID == self.UPI_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
geo = wk.inspector.currentGeometry
geoItem = wk.inspector.currentGeometryItem
geo.update()
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... update geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("geo.update()")
macro_script.append("wk.Refresh(inspector=True)")
macro_script.append("# ...")
wk.Refresh(inspector=True)
if ID == self.T5P_ID:
# inspector = self.parent
wk = self.parent.WorkGroup
item = wk.inspector.tree.GetSelection()
geo_bnd = wk.inspector.tree.GetItemData(item)
face = geo_bnd.face
faceItem = wk.inspector.tree.GetItemParent(item)
patchItem = wk.inspector.tree.GetItemParent(faceItem)
geoItem = wk.inspector.tree.GetItemParent(patchItem)
geo = wk.inspector.tree.GetItemData(geoItem)
_geo = cad_geometry()
_geo.append(geo[0])
geo_new = geometry(_geo.to5patchs(face))
geo_newItem = wk.add_geometry(geo_new)
# macro recording
if wk.macroRecording:
macro_script = wk.macro_script
macro_script.new_line()
macro_script.append("# ... to-5-patchs geometry")
geo_id = wk.list_geo.index(geo)
macro_script.append("geo_id = " + str(geo_id))
macro_script.append("geo = geometries[geo_id]")
macro_script.append("_geo = cad_geometry()")
macro_script.append("_geo.append(geo[0])")
macro_script.append("face = " + str(face))
macro_script.append("_geo = _geo.to5patchs(face)")
macro_script.append("wk.add_geometry(geometry(_geo))")
macro_script.append("wk.Refresh()")
macro_script.append("# ...")
wk.Refresh()
def main():
## trjconv -f 2LZM_wt.trr -o 2LZM_wt_trjconv.pdb -s 2LZM_wt_MD.tpr -skip 10 -sep
fd = open('2lzm.pdb','r')
lines1 = fd.readlines()
fd.close()
lines2 = []
for line in lines1:
record = line[:6].strip()
if record in ['HELIX','TURN','SHEET',]:
lines2 += [line]
for i in range(50):
fd = open('%i.pdb' %(i),'r')
lines = fd.readlines()
fd.close()
lines = lines2+lines
fd = open('nma%i.pdb' %(i),'w')
fd.writelines(lines)
fd.close()
stop
import sys, os, numpy
sys.path.append('/home/people/tc/svn/tc_sandbox/quakes/')
import phipsi_comparison
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import phipsi_plot
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
d_residues = {
'ALA':'A','CYS':'C','ASP':'D','GLU':'E','PHE':'F',
'GLY':'G','HIS':'H','ILE':'I','LYS':'K','LEU':'L',
'MET':'M','ASN':'N','PRO':'P','GLN':'Q','ARG':'R',
'SER':'S','THR':'T','VAL':'V','TRP':'W','TYR':'Y',
}
d_max = {}
d_ramachandran = {}
for res in d_residues.values():
d_ramachandran[res] = {}
for phi in range(-180,180):
d_ramachandran[res][phi] = {}
for psi in range(-180,180):
d_ramachandran[res][phi][psi] = 0
d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues) ## slow
## d_ramachandran[res][phi][psi] = 1
for res in d_ramachandran.keys():
max = 0
for phi in d_ramachandran[res].keys():
for psi in d_ramachandran[res][phi].keys():
count = d_ramachandran[res][phi][psi]
if count > max:
max = count
d_max[res] = max
option = 'gromacs'
option = 'pdbs'
if option == 'frames':
l = range(50)
elif option == 'pdbs':
l = ['150l',]
chain = 'D'
elif option == 'gromacs':
l = []
for i in range(101):
l += ['2LZM_wt_trjconv_%i' %(i)]
chain = ' '
fd = open('2LZM_wt_trjconv_0.pdb','r')
lines = fd.readlines()
fd.close()
l_coords_ref = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA':
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([x,y,z,])
l_coords_ref += [coord]
d_transformations = {}
for pdb in l:
if pdb == '2LZM_wt_trjconv_0.pdb':
continue
fd = open('%s.pdb' %(pdb),'r')
lines = fd.readlines()
fd.close()
l_coords = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA' and line[21] == chain:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([x,y,z,])
l_coords += [coord]
l_coords_ref = l_coords_ref[:len(l_coords)]
rmsd = instance_geometry.superpose(l_coords_ref,l_coords)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
d_transformations[pdb] = [tv1,rm,tv2,]
for pdb in l:
print pdb
if option == 'gromacs':
## i = int(pdb[pdb.rindex('_')+1:])
prefix = 'rasmol%s' %(i)
else:
prefix = 'rasmol%s' %(pdb)
lines_rotated = []
## write rasmol script
lines_rasmol = [
'rasmol -nodisplay %s_rotated.pdb << EOF\n' %(pdb),
'cartoon\n',
'wireframe 0\n',
]
d_phipsi, lines_gnuplot = phipsi_plot.calculate_phipsi(pdb, chain = chain)
fd = open('%s.pdb' %(pdb))
lines1 = fd.readlines()
fd.close()
for line1 in lines1:
record = line1[:6].strip()
if record in ['HELIX','TURN','SHEET',]:
lines_rotated += [line1]
if record != 'ATOM':
continue
if line1[21] != chain:
continue
atom_name = line1[12:16].strip()
## if atom_name != 'CA':
## continue
if atom_name not in ['N','CA','C','O',]:
continue
bfactor = float(line1[60:66])
res_no = int(line1[22:26])
res_name = line1[17:20].strip()
if res_no not in d_phipsi.keys():
bfactor = 50.
continue
else:
phi = int(d_phipsi[res_no][0])
psi = int(d_phipsi[res_no][1])
if phi == 180.:
phi = -180.
if psi == 180.:
psi = -180.
bfactor = (
100
*d_ramachandran[d_residues[res_name]][phi][psi]
/float(d_max[d_residues[res_name]])
)
x = float(line1[30:38])
y = float(line1[38:46])
z = float(line1[46:54])
coordinate = numpy.array([x,y,z,])
if pdb != '2LZM_wt_trjconv_0':
tv1 = d_transformations[pdb][0]
rm = d_transformations[pdb][1]
tv2 = d_transformations[pdb][2]
coordinate = numpy.dot(coordinate-tv1,rm)+tv2
lines_rotated += ['%s%8.3f%8.3f%8.3f%s%6.2f%s' %(
line1[:30],
coordinate[0],coordinate[1],coordinate[2],
line1[54:60],bfactor,line1[66:]
)]
h = 159.+80*bfactor/100.
s = 240.
l = 120.+120.*(50-abs(bfactor-50))/50.
r,g,b = hsl2rgb(h,s,l,)
lines_rasmol += [
'select %i\n' %(res_no),
'color [%i,%i,%i]\n' %(
r, g, b,
)
]
fd = open('%s_rotated.pdb' %(pdb),'w')
fd.writelines(lines_rotated)
fd.close()
lines_rasmol += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write %s.ppm\n' %(prefix),
'exit\n',
]
## write rasmol script to file
fd = open('%srasmol.src' %(prefix),'w')
fd.writelines(lines_rasmol)
fd.close()
## execute rasmol script
os.system('source %srasmol.src > %srasmol.log' %(prefix,prefix))
## convert rasmol output
## os.system('convert %s.ppm -resize x80 %s.gif' %(prefix,prefix))
os.system('convert %s.ppm %s.gif' %(prefix,prefix))
## clean up
os.remove('%s.ppm' %(prefix))
os.remove('%srasmol.log' %(prefix))
os.remove('%srasmol.src' %(prefix))
## os.remove('frame%s.pdb' %(str(i).zfill(2)))
if option == 'gromacs':
line = 'convert '
for i in range(101): ## 0 to 100
line += 'rasmol%s.gif ' %(i)
for i in range(101-1-1,-1+1,-1): ## 99 to 1
line += 'rasmol%s.gif ' %(i)
line += '-loop 0 2lzm_MD.gif'
print line
os.system(line)
## for frame in range(50):
## os.remove('rasmol%s.gif' %(i))
return
def main():
## trjconv -f 2LZM_wt.trr -o 2LZM_wt_trjconv.pdb -s 2LZM_wt_MD.tpr -skip 10 -sep
fd = open('2lzm.pdb', 'r')
lines1 = fd.readlines()
fd.close()
lines2 = []
for line in lines1:
record = line[:6].strip()
if record in [
'HELIX',
'TURN',
'SHEET',
]:
lines2 += [line]
for i in range(50):
fd = open('%i.pdb' % (i), 'r')
lines = fd.readlines()
fd.close()
lines = lines2 + lines
fd = open('nma%i.pdb' % (i), 'w')
fd.writelines(lines)
fd.close()
stop
import sys, os, numpy
sys.path.append('/home/people/tc/svn/tc_sandbox/quakes/')
import phipsi_comparison
sys.path.append('/home/people/tc/svn/tc_sandbox/misc/')
import phipsi_plot
sys.path.append('/home/people/tc/svn/Protool/')
import geometry
instance_geometry = geometry.geometry()
d_residues = {
'ALA': 'A',
'CYS': 'C',
'ASP': 'D',
'GLU': 'E',
'PHE': 'F',
'GLY': 'G',
'HIS': 'H',
'ILE': 'I',
'LYS': 'K',
'LEU': 'L',
'MET': 'M',
'ASN': 'N',
'PRO': 'P',
'GLN': 'Q',
'ARG': 'R',
'SER': 'S',
'THR': 'T',
'VAL': 'V',
'TRP': 'W',
'TYR': 'Y',
}
d_max = {}
d_ramachandran = {}
for res in d_residues.values():
d_ramachandran[res] = {}
for phi in range(-180, 180):
d_ramachandran[res][phi] = {}
for psi in range(-180, 180):
d_ramachandran[res][phi][psi] = 0
d_ramachandran = phipsi_comparison.parse_dihedrals(d_residues) ## slow
## d_ramachandran[res][phi][psi] = 1
for res in d_ramachandran.keys():
max = 0
for phi in d_ramachandran[res].keys():
for psi in d_ramachandran[res][phi].keys():
count = d_ramachandran[res][phi][psi]
if count > max:
max = count
d_max[res] = max
option = 'gromacs'
option = 'pdbs'
if option == 'frames':
l = range(50)
elif option == 'pdbs':
l = [
'150l',
]
chain = 'D'
elif option == 'gromacs':
l = []
for i in range(101):
l += ['2LZM_wt_trjconv_%i' % (i)]
chain = ' '
fd = open('2LZM_wt_trjconv_0.pdb', 'r')
lines = fd.readlines()
fd.close()
l_coords_ref = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA':
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([
x,
y,
z,
])
l_coords_ref += [coord]
d_transformations = {}
for pdb in l:
if pdb == '2LZM_wt_trjconv_0.pdb':
continue
fd = open('%s.pdb' % (pdb), 'r')
lines = fd.readlines()
fd.close()
l_coords = []
for line in lines:
record = line[:6].strip()
if record == 'ATOM':
atom_name = line[12:16].strip()
if atom_name == 'CA' and line[21] == chain:
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
coord = numpy.array([
x,
y,
z,
])
l_coords += [coord]
l_coords_ref = l_coords_ref[:len(l_coords)]
rmsd = instance_geometry.superpose(l_coords_ref, l_coords)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
d_transformations[pdb] = [
tv1,
rm,
tv2,
]
for pdb in l:
print pdb
if option == 'gromacs':
## i = int(pdb[pdb.rindex('_')+1:])
prefix = 'rasmol%s' % (i)
else:
prefix = 'rasmol%s' % (pdb)
lines_rotated = []
## write rasmol script
lines_rasmol = [
'rasmol -nodisplay %s_rotated.pdb << EOF\n' % (pdb),
'cartoon\n',
'wireframe 0\n',
]
d_phipsi, lines_gnuplot = phipsi_plot.calculate_phipsi(pdb,
chain=chain)
fd = open('%s.pdb' % (pdb))
lines1 = fd.readlines()
fd.close()
for line1 in lines1:
record = line1[:6].strip()
if record in [
'HELIX',
'TURN',
'SHEET',
]:
lines_rotated += [line1]
if record != 'ATOM':
continue
if line1[21] != chain:
continue
atom_name = line1[12:16].strip()
## if atom_name != 'CA':
## continue
if atom_name not in [
'N',
'CA',
'C',
'O',
]:
continue
bfactor = float(line1[60:66])
res_no = int(line1[22:26])
res_name = line1[17:20].strip()
if res_no not in d_phipsi.keys():
bfactor = 50.
continue
else:
phi = int(d_phipsi[res_no][0])
psi = int(d_phipsi[res_no][1])
if phi == 180.:
phi = -180.
if psi == 180.:
psi = -180.
bfactor = (100 *
d_ramachandran[d_residues[res_name]][phi][psi] /
float(d_max[d_residues[res_name]]))
x = float(line1[30:38])
y = float(line1[38:46])
z = float(line1[46:54])
coordinate = numpy.array([
x,
y,
z,
])
if pdb != '2LZM_wt_trjconv_0':
tv1 = d_transformations[pdb][0]
rm = d_transformations[pdb][1]
tv2 = d_transformations[pdb][2]
coordinate = numpy.dot(coordinate - tv1, rm) + tv2
lines_rotated += [
'%s%8.3f%8.3f%8.3f%s%6.2f%s' %
(line1[:30], coordinate[0], coordinate[1], coordinate[2],
line1[54:60], bfactor, line1[66:])
]
h = 159. + 80 * bfactor / 100.
s = 240.
l = 120. + 120. * (50 - abs(bfactor - 50)) / 50.
r, g, b = hsl2rgb(
h,
s,
l,
)
lines_rasmol += [
'select %i\n' % (res_no),
'color [%i,%i,%i]\n' % (
r,
g,
b,
)
]
fd = open('%s_rotated.pdb' % (pdb), 'w')
fd.writelines(lines_rotated)
fd.close()
lines_rasmol += [
## 'ribbons\n',
'rotate x 100\n',
'rotate z 30\n',
'rotate x 100\n',
'rotate z 90\n',
'rotate x 40\n',
'rotate y -20\n',
'write %s.ppm\n' % (prefix),
'exit\n',
]
## write rasmol script to file
fd = open('%srasmol.src' % (prefix), 'w')
fd.writelines(lines_rasmol)
fd.close()
## execute rasmol script
os.system('source %srasmol.src > %srasmol.log' % (prefix, prefix))
## convert rasmol output
## os.system('convert %s.ppm -resize x80 %s.gif' %(prefix,prefix))
os.system('convert %s.ppm %s.gif' % (prefix, prefix))
## clean up
os.remove('%s.ppm' % (prefix))
os.remove('%srasmol.log' % (prefix))
os.remove('%srasmol.src' % (prefix))
## os.remove('frame%s.pdb' %(str(i).zfill(2)))
if option == 'gromacs':
line = 'convert '
for i in range(101): ## 0 to 100
line += 'rasmol%s.gif ' % (i)
for i in range(101 - 1 - 1, -1 + 1, -1): ## 99 to 1
line += 'rasmol%s.gif ' % (i)
line += '-loop 0 2lzm_MD.gif'
print line
os.system(line)
## for frame in range(50):
## os.remove('rasmol%s.gif' %(i))
return
def solve_steady(self):
"""
function: solve_steady
Solves for the steady state solution
Parameters:
-None
Returns:
-None
"""
self.logger.info('Starting steady state solving...')
self.logger.info('Setting the geometry...')
self.geom = geometry(self.config['Bfield'], self.config['delta'],
self.config['R'], self.config['d'],
self.config['z'])
self.logger.info('Geometry set')
self.logger.info('The initial electron spectrum...')
self.__init_spectrum('11')
self.logger.info('Set the initial spectrum')
# Synchrotron
self.logger.info('Synchrotron...')
A = self.geom.A
self.particles['22_local'].flux['0'] = np.zeros(
config['grid_22_local'])
# transition from electron_j to gamma_i
self.particles['22_local'].flux['0'] = \
A * np.dot(self.synch_rate,
self.particles['11'].flux['0'] /
self.particles['11'].e_diff) / self.particles['22'].e_diff
# This is not implemented in Damien's code
# Also not sure what type of function onemexpdexp is,
# it is not implemented in Damien's code
# Opacity
# ASSA = self.geom.ASSA
# tauCst = self.geom.tauCst
# for i in range(0, config['grid 22']):
# summtau = 0.
# for j in range(0, config['grid 11']):
# summtau += (self.opacity_rate[i][j] *
# (self.particles['11'].flux['0'][j] /
# (self.particles['11'].e_borders[j+1] -
# self.particles['11'].e_borders[j])))
# summtau = ASSA*tauCst*summtau
# self.particles['22'].flux['0'][i] = (
# self.particles['22'].flux['0'][i] * onemexpdexp(summtau)
# )
# IC
self.logger.info('Inverse Compton...')
self.particles['22_local'].flux['2'] = np.zeros(
config['grid_22_local'])
self.particles['22'].flux['0'] = np.zeros(config['grid_22'])
self.particles['22'].flux['2'] = np.zeros(config['grid_22'])
# Rescaling the photon grid according to the local version
self.rescale('22_local', '22')
summIC = np.zeros(config['grid_22'])
for i in range(0, config['grid_22']):
# This is now a matrix vector multiplication
term = (
np.dot(
self.IC_rate[i, :, :, 0], # * mask,
self.particles['11'].flux['0'] /
self.particles['11'].e_diff))
summIC[i] = np.sum(self.particles['22'].flux['0'] * term)
summICfinal = (0.75 * phys_const['c'] * phys_const['sigmaT'] * summIC /
self.particles['22'].e_diff)
# Multiply the emissivity by the volume.
self.particles['22'].flux['2'] = (
(4. * pi * self.geom.R**3 * self.geom.delta**3 /
(self.geom.d**2 * unit_conv['Mpc_to_cm']**2 * 4. * pi * 3.)) *
((self.geom.R / phys_const['c']) * summICfinal) * phys_const['h'] *
self.particles['22'].e_grid)
self.particles['22'].flux['0'] = (
(4. * pi * self.geom.R**3 * self.geom.delta**3 /
(self.geom.d**2 * unit_conv['Mpc_to_cm']**2 * 4. * pi * 3.)) *
self.particles['22'].flux['0'] * phys_const['h'] *
self.particles['22'].e_grid)
# Pair
# Is not implemented
# Normalizing pre-storage
# Todo: Why? Think this is causes a problem when
# changing parameters and refitting
self.particles['22'].e_grid = (self.particles['22'].e_grid *
self.geom.delta / (1. + self.geom.z))
# Storing results
self.logger.info('Storing results...')
saveString = '../data/results.pkl'
with open(saveString, 'wb') as f:
cPickle.dump(self.particles, f, protocol=cPickle.HIGHEST_PROTOCOL)
# Load with
# with open(saveString, 'rb') as f:
# self.particles = cPickle.load(f)
self.logger.info('Finished steady state solving...')
self.logger.info('Results stored in particle fluxes...')
handlers = self.logger.handlers[:]
for handler in handlers:
handler.close()
self.logger.removeHandler(handler)
def main(
self, jobid, lines, atoms_hessian = ['CA'], frames = 50,
cutoff_distance = 10.,
path_python = None, verbose = False, paralleldir = '',
biomolecule = None, chains = [], model = None,
):
'''
Use first model if no model specified by user.
chain(s): Y, biomolecule: Y; parse chains specified by user and apply transformation
chain(s): Y, biomolecule: N; parse chains specified by user but don't apply transformation
chain(s): N, biomolecule: Y; parse chains of biomolecule and apply transformation
chain(s): N, biomolecule: N; parse chains of first biomolecule and apply transformation
'''
import os, Numeric, goodvibes_core
results = []
## parse pdb
(
d_REMARK350,
d_primary, ## i.e. SEQRES, MODRES
d_secondary, ## i.e. HELIX, SHEET
d_coordinates, ## i.e. ATOM, HETATM, TER, MODEL, ENDMDL
d_ligands,
) = goodvibes_core.parse_pdb(lines, chains)
## assume multimeric biological unit if chains not specified by user
if chains == []:
chains = d_coordinates['chains'].keys()
chains.sort()
##
## calculate N and convert coordinates from dic to list
##
N, d_hessian, l_coordinates = goodvibes_core.parse_dictionary_of_coordinates(d_coordinates, chains, atoms_hessian)
##
## calculate distance matrix
##
matrix_distances = goodvibes_core.calculate_distance_matrix(l_coordinates)
##
## calculate hessian matrix
##
matrix_hessian = self.hessian_calculation(N, d_coordinates, chains, atoms_hessian, float(cutoff_distance), d_secondary, matrix_distances, l_coordinates, verbose = verbose)
##
## diagonalize hessian matrix
##
eigenvectors_nonperturbed, eigenvalues_nonperturbed, eigenvectors_comb_nonperturbed, = goodvibes_core.eigenv_calccomb(
matrix_hessian, jobid, verbose,
)
## fd = open('/oxygenase_local/data/pdb/50/pdb150l.ent','r')
fd = open('/oxygenase_local/data/pdb/lz/pdb2lzm.ent','r')
lines = fd.readlines()
fd.close()
(
d_REMARK350,
d_primary, ## i.e. SEQRES, MODRES
d_secondary, ## i.e. HELIX, SHEET
d_coordinates, ## i.e. ATOM, HETATM, TER, MODEL, ENDMDL
d_ligands,
) = goodvibes_core.parse_pdb(lines, chains)
N, d_hessian, l_coordinates2 = goodvibes_core.parse_dictionary_of_coordinates(d_coordinates, chains, atoms_hessian)
if len(l_coordinates) != len(l_coordinates2):
print len(l_coordinates), len(l_coordinates2)
stop
## import geometry
import sys
sys.path.append('/home/people/tc/svn/Protool/trunk/')
import geometry
instance_geometry = geometry.geometry()
## superpose
rmsd = instance_geometry.superpose(l_coordinates,l_coordinates2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
print rmsd
## calculate differences
l_differences = []
for i in range(len(l_coordinates)):
coord1 = l_coordinates[i]
coord2 = Numeric.matrixmultiply(l_coordinates2[i]-tv1,rm)+tv2
l_differences += [
coord1[0]-coord2[0],
coord1[1]-coord2[1],
coord1[2]-coord2[2],
]
vector_difference = Numeric.array(l_differences)
import math
for mode in range(20):
vector_nonperturbed = eigenvectors_nonperturbed[mode]
overlap = math.fabs(goodvibes_core.cosangle(vector_nonperturbed, vector_difference))
overlaps = []
for i in range(0,164,3):
numerator = (
vector_nonperturbed[i+0]*vector_difference[i+0]+
vector_nonperturbed[i+1]*vector_difference[i+1]+
vector_nonperturbed[i+2]*vector_difference[i+2]
)
denominator = (
math.sqrt(vector_nonperturbed[i+0]**2+vector_nonperturbed[i+1]**2+vector_nonperturbed[i+2]**2)*
math.sqrt(vector_difference[i+0]**2+vector_difference[i+1]**2+vector_difference[i+2]**2)
)
overlaps += [numerator/denominator]
if mode == 6:
print sum(overlaps)/len(overlaps)
print mode, overlap
stop
##
## visualize eigenvectors
##
goodvibes_core.morph(
eigenvectors_nonperturbed, frames, chains, d_coordinates,
jobid, d_primary,
)
##
## do plots prior to perturbation
##
## goodvibes_core.pre_perturbation_plot(
## jobid,cutoff_distance,chains,d_secondary,
## eigenvectors_nonperturbed,eigenvectors_comb_nonperturbed,
## )
##
## set data lists and append matrices to be plotted for each combination of modes 6-12 before initiating loops over the two axes of the plot
##
datadic = goodvibes_core.datadic_return(N)
return
